BBMap SNP call pipeline from WGS or RNA-seq data
>h1tg000001l
ATCTTCAAACCAACTGCGCCCACACCCACTTTCATCATTTCTCCAGACGATAGGGCATTA
ATCATGGCACGGTTCACTGTAATTGAAAATCTTGTATCAGATGGTTTACTAGCATAAGTG
TGTGTTTAATTTTGCAATACGCTTTCCTCACATCTTTGTTCTTAGTGTTGAGGTTGCAGT
GCTCACCATACATCAATTCATAAGTGATTAGAAGAGACAGAGAACAAGGGGCAATAGCAA
AGCATTTGCTCACTTTGGCACCATTCGGACTGCACTCAATAGTTTATATGGTTTAATAAT
CATCCCTGCATATATCATGCAAGAACTCTTTGAATTTGTAATCACCGTGCATGCACACTT
TCGCCAAATTTCTATGGCAAGTCTGCATTGATTCCTTTTTGCTCAACGGATCACTAATTG
TCCTGTATAGTTAGAGCCCGTTCACAAACCTCGCACAGGCAAATCACCTGCAAAGGTCAA
CATCGTTTTCAACGTCAGCGGAGCAATGTTGAACTAAAATTAGCATACTCTAAAAGAATG
RNA-seq~SNPcall-bbmap-callvariants -c 16 -m 128 input_1/ input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
##fileformat=VCFv4.2
##BBMapVersion=38.96
##ploidy=2
##rarity=1.00000
##minallelefraction=0.10000
##reads=703054
##pairedReads=703054
##properlyPairedReads=624842
##properPairRate=0.8888
##readLengthAvg=140.87
pp RNA-seq~SNPcall-bbmap-callvariants -c 16 -m 128 input_1/ input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-1-501-701_1.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-1-501-701_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-12-501-708_1.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-12-501-708_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-17-502-703_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-13-502-701_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-17-502-703_1.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-13-502-701_1.fastq.gz
0 input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
script: /yoshitake/PortablePipeline/PortablePipeline/scripts/RNA-seq~SNPcall-bbmap-callvariants "$scriptdir"/mapping-illumina~bbmap
broadinstitute/gatk:4.3.0.0 centos:centos6 quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 quay.io/biocontainers/picard:2.18.27--0
using docker
+ set -o pipefail
++ date +%s
+ time0=1677603411
+ echo start at 1677603411
start at 1677603411
+ bash /yoshitake/PortablePipeline/PortablePipeline/scripts/mapping-illumina~bbmap -c 16 -m 128 -i '' -j 'maxindel=100000 maxsites2=10000' -b ON -o '' input_1/ input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-1-501-701_1.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-1-501-701_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-12-501-708_1.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-12-501-708_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-17-502-703_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-13-502-701_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-17-502-703_1.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-13-502-701_1.fastq.gz
0 input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
broadinstitute/gatk:4.3.0.0 centos:centos6 quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 quay.io/biocontainers/picard:2.18.27--0
using docker
+ set -o pipefail
+ exec
++ tee log.txt
+ LANG=C
+ threads=16
+ three=16
++ expr 16 / 2
+ threads2=8
++ expr 16 - 2
+ threads1=14
+ '[' 14 -lt 1 ']'
++ free -g
++ grep Mem
++ sed -e 's/Mem: *\([0-9]*\) .*/\1/'
+ memG=251
++ expr 251 '*' 3 / 4
+ memG3=188
+ echo '
#####SYSTEM ENVIRONMENT#####
threads=16
memory=251G
############################
'
#####SYSTEM ENVIRONMENT#####
threads=16
memory=251G
############################
++ date +%s
+ time0=1677603411
+ echo start at 1677603411
start at 1677603411
+ echo -e 'Checking paramter settings...\n'
Checking paramter settings...
+ indexing_param=k=13
+ mapping_param='maxindel=100000 maxsites2=10000'
+ out_files=
+ for i in '$opt_o'
+ out_files+=' rpkm=rpkm.tsv'
+ for i in '$opt_o'
+ out_files+=' covstats=covstats.tsv'
+ mapped_only_bam=ON
++ echo input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
+ ref=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
+ FUNC_RUN_DOCKER quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 bbmap.sh threads=16 k=13 ref=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
+ PP_RUN_IMAGE=quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230301_015651_639_11352
+ echo pp20230301_015651_639_11352
++ id -u
++ id -g
+ docker run --name pp20230301_015651_639_11352 -v /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants:/yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants -w /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 bbmap.sh threads=16 k=13 ref=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
java -ea -Xmx109177m -Xms109177m -cp /usr/local/opt/bbmap-38.96-1/current/ align2.BBMap build=1 overwrite=true fastareadlen=500 threads=16 k=13 ref=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, threads=16, k=13, ref=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta]
Version 38.96
Set threads to 16
No output file.
NOTE: Ignoring reference file because it already appears to have been processed.
NOTE: If you wish to regenerate the index, please manually delete ref/genome/1/summary.txt
Set genome to 1
Loaded Reference: 0.393 seconds.
Loading index for chunk 1-1, build 1
Generated Index: 1.168 seconds.
No reads to process; quitting.
Total time: 1.686 seconds.
+ cat
+ pppair1=()
+ pppair2=()
+ ppsingle=()
+ IFS=
+ read i
++ find input_1//
++ egrep '(_R1.*|_1)[.]f((ast|)(q|a)|na|sa)(|[.]gz)$'
++ echo input_1//Le1-1-501-701_1.fastq.gz
++ egrep '_1[.]f((ast|)(q|a)|na|sa)(|[.]gz)$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo input_1//Le1-1-501-701_1.fastq.gz
++ sed 's/_1[.]\(f\(\(ast\|\)\(q\|a\)\|na\|sa\)\(\|[.]gz\)\)$/_2.\1/'
+ temppair2=input_1//Le1-1-501-701_2.fastq.gz
+ '[' -e input_1//Le1-1-501-701_2.fastq.gz ']'
+ pppair1+=("$i")
+ pppair2+=("$temppair2")
+ IFS=
+ read i
++ echo input_1//Le1-12-501-708_1.fastq.gz
++ egrep '_1[.]f((ast|)(q|a)|na|sa)(|[.]gz)$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo input_1//Le1-12-501-708_1.fastq.gz
++ sed 's/_1[.]\(f\(\(ast\|\)\(q\|a\)\|na\|sa\)\(\|[.]gz\)\)$/_2.\1/'
+ temppair2=input_1//Le1-12-501-708_2.fastq.gz
+ '[' -e input_1//Le1-12-501-708_2.fastq.gz ']'
+ pppair1+=("$i")
+ pppair2+=("$temppair2")
+ IFS=
+ read i
++ echo input_1//Le1-17-502-703_1.fastq.gz
++ egrep '_1[.]f((ast|)(q|a)|na|sa)(|[.]gz)$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo input_1//Le1-17-502-703_1.fastq.gz
++ sed 's/_1[.]\(f\(\(ast\|\)\(q\|a\)\|na\|sa\)\(\|[.]gz\)\)$/_2.\1/'
+ temppair2=input_1//Le1-17-502-703_2.fastq.gz
+ '[' -e input_1//Le1-17-502-703_2.fastq.gz ']'
+ pppair1+=("$i")
+ pppair2+=("$temppair2")
+ IFS=
+ read i
++ echo input_1//Le1-13-502-701_1.fastq.gz
++ egrep '_1[.]f((ast|)(q|a)|na|sa)(|[.]gz)$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo input_1//Le1-13-502-701_1.fastq.gz
++ sed 's/_1[.]\(f\(\(ast\|\)\(q\|a\)\|na\|sa\)\(\|[.]gz\)\)$/_2.\1/'
+ temppair2=input_1//Le1-13-502-701_2.fastq.gz
+ '[' -e input_1//Le1-13-502-701_2.fastq.gz ']'
+ pppair1+=("$i")
+ pppair2+=("$temppair2")
+ IFS=
+ read i
+ IFS=
+ read i
++ find input_1//
++ egrep '[.]f((ast|)(q|a)|na|sa)(|[.]gz)$'
+ ppinputcheck=0
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-1-501-701_1.fastq.gz = input_1//Le1-1-501-701_1.fastq.gz ']'
+ ppinputcheck=1
+ break
+ '[' 1 = 0 ']'
+ IFS=
+ read i
+ ppinputcheck=0
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-1-501-701_1.fastq.gz = input_1//Le1-1-501-701_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-12-501-708_1.fastq.gz = input_1//Le1-1-501-701_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-17-502-703_1.fastq.gz = input_1//Le1-1-501-701_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-13-502-701_1.fastq.gz = input_1//Le1-1-501-701_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-1-501-701_2.fastq.gz = input_1//Le1-1-501-701_2.fastq.gz ']'
+ ppinputcheck=1
+ break
+ '[' 1 = 0 ']'
+ IFS=
+ read i
+ ppinputcheck=0
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-1-501-701_1.fastq.gz = input_1//Le1-12-501-708_1.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-12-501-708_1.fastq.gz = input_1//Le1-12-501-708_1.fastq.gz ']'
+ ppinputcheck=1
+ break
+ '[' 1 = 0 ']'
+ IFS=
+ read i
+ ppinputcheck=0
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-1-501-701_1.fastq.gz = input_1//Le1-12-501-708_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-12-501-708_1.fastq.gz = input_1//Le1-12-501-708_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-17-502-703_1.fastq.gz = input_1//Le1-12-501-708_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-13-502-701_1.fastq.gz = input_1//Le1-12-501-708_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-1-501-701_2.fastq.gz = input_1//Le1-12-501-708_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-12-501-708_2.fastq.gz = input_1//Le1-12-501-708_2.fastq.gz ']'
+ ppinputcheck=1
+ break
+ '[' 1 = 0 ']'
+ IFS=
+ read i
+ ppinputcheck=0
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-1-501-701_1.fastq.gz = input_1//Le1-17-502-703_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-12-501-708_1.fastq.gz = input_1//Le1-17-502-703_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-17-502-703_1.fastq.gz = input_1//Le1-17-502-703_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-13-502-701_1.fastq.gz = input_1//Le1-17-502-703_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-1-501-701_2.fastq.gz = input_1//Le1-17-502-703_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-12-501-708_2.fastq.gz = input_1//Le1-17-502-703_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-17-502-703_2.fastq.gz = input_1//Le1-17-502-703_2.fastq.gz ']'
+ ppinputcheck=1
+ break
+ '[' 1 = 0 ']'
+ IFS=
+ read i
+ ppinputcheck=0
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-1-501-701_1.fastq.gz = input_1//Le1-13-502-701_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-12-501-708_1.fastq.gz = input_1//Le1-13-502-701_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-17-502-703_1.fastq.gz = input_1//Le1-13-502-701_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-13-502-701_1.fastq.gz = input_1//Le1-13-502-701_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-1-501-701_2.fastq.gz = input_1//Le1-13-502-701_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-12-501-708_2.fastq.gz = input_1//Le1-13-502-701_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-17-502-703_2.fastq.gz = input_1//Le1-13-502-701_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-13-502-701_2.fastq.gz = input_1//Le1-13-502-701_2.fastq.gz ']'
+ ppinputcheck=1
+ break
+ '[' 1 = 0 ']'
+ IFS=
+ read i
+ ppinputcheck=0
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-1-501-701_1.fastq.gz = input_1//Le1-17-502-703_1.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-12-501-708_1.fastq.gz = input_1//Le1-17-502-703_1.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-17-502-703_1.fastq.gz = input_1//Le1-17-502-703_1.fastq.gz ']'
+ ppinputcheck=1
+ break
+ '[' 1 = 0 ']'
+ IFS=
+ read i
+ ppinputcheck=0
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-1-501-701_1.fastq.gz = input_1//Le1-13-502-701_1.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-12-501-708_1.fastq.gz = input_1//Le1-13-502-701_1.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-17-502-703_1.fastq.gz = input_1//Le1-13-502-701_1.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-13-502-701_1.fastq.gz = input_1//Le1-13-502-701_1.fastq.gz ']'
+ ppinputcheck=1
+ break
+ '[' 1 = 0 ']'
+ IFS=
+ read i
+ mkdir -p output
+ (( i = 0 ))
+ xargs '-d\n' -I '{}' -P 1 bash -c '{}'
+ (( i < 4 ))
++ basename input_1//Le1-1-501-701_1.fastq.gz
+ prefix=output/Le1-1-501-701_1.fastq.gz
+ local_out_files=' rpkm=output/Le1-1-501-701_1.fastq.gz_rpkm.tsv covstats=output/Le1-1-501-701_1.fastq.gz_covstats.tsv'
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 bbmap.sh ref="input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta" threads="14" in1="input_1//Le1-1-501-701_1.fastq.gz" in2="input_1//Le1-1-501-701_2.fastq.gz" out="output/Le1-1-501-701_1.fastq.gz".temp.bam maxindel=100000 maxsites2=10000 rpkm=output/Le1-1-501-701_1.fastq.gz_rpkm.tsv covstats=output/Le1-1-501-701_1.fastq.gz_covstats.tsv; PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 bash run-samtools.sh "output/Le1-1-501-701_1.fastq.gz".temp.bam "14" "ON" "6553"'
+ (( i++ ))
+ (( i < 4 ))
++ basename input_1//Le1-12-501-708_1.fastq.gz
+ prefix=output/Le1-12-501-708_1.fastq.gz
+ local_out_files=' rpkm=output/Le1-12-501-708_1.fastq.gz_rpkm.tsv covstats=output/Le1-12-501-708_1.fastq.gz_covstats.tsv'
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 bbmap.sh ref="input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta" threads="14" in1="input_1//Le1-12-501-708_1.fastq.gz" in2="input_1//Le1-12-501-708_2.fastq.gz" out="output/Le1-12-501-708_1.fastq.gz".temp.bam maxindel=100000 maxsites2=10000 rpkm=output/Le1-12-501-708_1.fastq.gz_rpkm.tsv covstats=output/Le1-12-501-708_1.fastq.gz_covstats.tsv; PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 bash run-samtools.sh "output/Le1-12-501-708_1.fastq.gz".temp.bam "14" "ON" "6553"'
+ (( i++ ))
+ (( i < 4 ))
++ basename input_1//Le1-17-502-703_1.fastq.gz
+ prefix=output/Le1-17-502-703_1.fastq.gz
+ local_out_files=' rpkm=output/Le1-17-502-703_1.fastq.gz_rpkm.tsv covstats=output/Le1-17-502-703_1.fastq.gz_covstats.tsv'
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 bbmap.sh ref="input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta" threads="14" in1="input_1//Le1-17-502-703_1.fastq.gz" in2="input_1//Le1-17-502-703_2.fastq.gz" out="output/Le1-17-502-703_1.fastq.gz".temp.bam maxindel=100000 maxsites2=10000 rpkm=output/Le1-17-502-703_1.fastq.gz_rpkm.tsv covstats=output/Le1-17-502-703_1.fastq.gz_covstats.tsv; PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 bash run-samtools.sh "output/Le1-17-502-703_1.fastq.gz".temp.bam "14" "ON" "6553"'
+ (( i++ ))
+ (( i < 4 ))
++ basename input_1//Le1-13-502-701_1.fastq.gz
+ prefix=output/Le1-13-502-701_1.fastq.gz
+ local_out_files=' rpkm=output/Le1-13-502-701_1.fastq.gz_rpkm.tsv covstats=output/Le1-13-502-701_1.fastq.gz_covstats.tsv'
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 bbmap.sh ref="input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta" threads="14" in1="input_1//Le1-13-502-701_1.fastq.gz" in2="input_1//Le1-13-502-701_2.fastq.gz" out="output/Le1-13-502-701_1.fastq.gz".temp.bam maxindel=100000 maxsites2=10000 rpkm=output/Le1-13-502-701_1.fastq.gz_rpkm.tsv covstats=output/Le1-13-502-701_1.fastq.gz_covstats.tsv; PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 bash run-samtools.sh "output/Le1-13-502-701_1.fastq.gz".temp.bam "14" "ON" "6553"'
+ (( i++ ))
+ (( i < 4 ))
java -ea -Xmx109179m -Xms109179m -cp /usr/local/opt/bbmap-38.96-1/current/ align2.BBMap build=1 overwrite=true fastareadlen=500 ref=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta threads=14 in1=input_1//Le1-1-501-701_1.fastq.gz in2=input_1//Le1-1-501-701_2.fastq.gz out=output/Le1-1-501-701_1.fastq.gz.temp.bam maxindel=100000 maxsites2=10000 rpkm=output/Le1-1-501-701_1.fastq.gz_rpkm.tsv covstats=output/Le1-1-501-701_1.fastq.gz_covstats.tsv
Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta, threads=14, in1=input_1//Le1-1-501-701_1.fastq.gz, in2=input_1//Le1-1-501-701_2.fastq.gz, out=output/Le1-1-501-701_1.fastq.gz.temp.bam, maxindel=100000, maxsites2=10000, rpkm=output/Le1-1-501-701_1.fastq.gz_rpkm.tsv, covstats=output/Le1-1-501-701_1.fastq.gz_covstats.tsv]
Version 38.96
Set threads to 14
Retaining first best site only for ambiguous mappings.
NOTE: Ignoring reference file because it already appears to have been processed.
NOTE: If you wish to regenerate the index, please manually delete ref/genome/1/summary.txt
Set genome to 1
Loaded Reference: 0.393 seconds.
Loading index for chunk 1-1, build 1
Generated Index: 1.164 seconds.
Analyzed Index: 3.715 seconds.
Found samtools 1.15
Started output stream: 0.078 seconds.
Cleared Memory: 0.213 seconds.
Processing reads in paired-ended mode.
Started read stream.
Started 14 mapping threads.
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-1-501-701_1.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-1-501-701_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-12-501-708_1.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-12-501-708_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-17-502-703_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-13-502-701_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-17-502-703_1.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-13-502-701_1.fastq.gz
0 input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
script: /yoshitake/PortablePipeline/PortablePipeline/scripts/RNA-seq~SNPcall-bbmap-callvariants "$scriptdir"/mapping-illumina~bbmap
broadinstitute/gatk:4.3.0.0 centos:centos6 quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 quay.io/biocontainers/picard:2.18.27--0
using docker
+ set -o pipefail
++ date +%s
+ time0=1677603490
+ echo start at 1677603490
start at 1677603490
+ bash /yoshitake/PortablePipeline/PortablePipeline/scripts/mapping-illumina~bbmap -c 16 -m 128 -i '' -j 'maxindel=100000 maxsites2=10000' -b ON -o ' ' input_1/ input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-1-501-701_1.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-1-501-701_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-12-501-708_1.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-12-501-708_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-17-502-703_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-13-502-701_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-17-502-703_1.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-13-502-701_1.fastq.gz
0 input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
broadinstitute/gatk:4.3.0.0 centos:centos6 quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 quay.io/biocontainers/picard:2.18.27--0
using docker
+ set -o pipefail
+ exec
++ tee log.txt
+ LANG=C
+ threads=16
+ three=16
++ expr 16 / 2
+ threads2=8
++ expr 16 - 2
+ threads1=14
+ '[' 14 -lt 1 ']'
++ free -g
++ grep Mem
++ sed -e 's/Mem: *\([0-9]*\) .*/\1/'
+ memG=251
++ expr 251 '*' 3 / 4
+ memG3=188
+ echo '
#####SYSTEM ENVIRONMENT#####
threads=16
memory=251G
############################
'
#####SYSTEM ENVIRONMENT#####
threads=16
memory=251G
############################
++ date +%s
+ time0=1677603491
+ echo start at 1677603491
start at 1677603491
+ echo -e 'Checking paramter settings...\n'
Checking paramter settings...
+ indexing_param=k=13
+ mapping_param='maxindel=100000 maxsites2=10000'
+ out_files=
+ mapped_only_bam=ON
++ echo input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
+ ref=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
+ FUNC_RUN_DOCKER quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 bbmap.sh threads=16 k=13 ref=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
+ PP_RUN_IMAGE=quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230301_015811_642_8631
+ echo pp20230301_015811_642_8631
++ id -u
++ id -g
+ docker run --name pp20230301_015811_642_8631 -v /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants:/yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants -w /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 bbmap.sh threads=16 k=13 ref=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
java -ea -Xmx109180m -Xms109180m -cp /usr/local/opt/bbmap-38.96-1/current/ align2.BBMap build=1 overwrite=true fastareadlen=500 threads=16 k=13 ref=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, threads=16, k=13, ref=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta]
Version 38.96
Set threads to 16
No output file.
NOTE: Ignoring reference file because it already appears to have been processed.
NOTE: If you wish to regenerate the index, please manually delete ref/genome/1/summary.txt
Set genome to 1
Loaded Reference: 0.388 seconds.
Loading index for chunk 1-1, build 1
Generated Index: 1.167 seconds.
No reads to process; quitting.
Total time: 1.679 seconds.
+ cat
+ pppair1=()
+ pppair2=()
+ ppsingle=()
+ IFS=
+ read i
++ find input_1//
++ egrep '(_R1.*|_1)[.]f((ast|)(q|a)|na|sa)(|[.]gz)$'
++ echo input_1//Le1-1-501-701_1.fastq.gz
++ egrep '_1[.]f((ast|)(q|a)|na|sa)(|[.]gz)$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo input_1//Le1-1-501-701_1.fastq.gz
++ sed 's/_1[.]\(f\(\(ast\|\)\(q\|a\)\|na\|sa\)\(\|[.]gz\)\)$/_2.\1/'
+ temppair2=input_1//Le1-1-501-701_2.fastq.gz
+ '[' -e input_1//Le1-1-501-701_2.fastq.gz ']'
+ pppair1+=("$i")
+ pppair2+=("$temppair2")
+ IFS=
+ read i
++ echo input_1//Le1-12-501-708_1.fastq.gz
++ egrep '_1[.]f((ast|)(q|a)|na|sa)(|[.]gz)$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo input_1//Le1-12-501-708_1.fastq.gz
++ sed 's/_1[.]\(f\(\(ast\|\)\(q\|a\)\|na\|sa\)\(\|[.]gz\)\)$/_2.\1/'
+ temppair2=input_1//Le1-12-501-708_2.fastq.gz
+ '[' -e input_1//Le1-12-501-708_2.fastq.gz ']'
+ pppair1+=("$i")
+ pppair2+=("$temppair2")
+ IFS=
+ read i
++ echo input_1//Le1-17-502-703_1.fastq.gz
++ egrep '_1[.]f((ast|)(q|a)|na|sa)(|[.]gz)$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo input_1//Le1-17-502-703_1.fastq.gz
++ sed 's/_1[.]\(f\(\(ast\|\)\(q\|a\)\|na\|sa\)\(\|[.]gz\)\)$/_2.\1/'
+ temppair2=input_1//Le1-17-502-703_2.fastq.gz
+ '[' -e input_1//Le1-17-502-703_2.fastq.gz ']'
+ pppair1+=("$i")
+ pppair2+=("$temppair2")
+ IFS=
+ read i
++ echo input_1//Le1-13-502-701_1.fastq.gz
++ wc -l
++ egrep '_1[.]f((ast|)(q|a)|na|sa)(|[.]gz)$'
+ '[' 1 = 1 ']'
++ echo input_1//Le1-13-502-701_1.fastq.gz
++ sed 's/_1[.]\(f\(\(ast\|\)\(q\|a\)\|na\|sa\)\(\|[.]gz\)\)$/_2.\1/'
+ temppair2=input_1//Le1-13-502-701_2.fastq.gz
+ '[' -e input_1//Le1-13-502-701_2.fastq.gz ']'
+ pppair1+=("$i")
+ pppair2+=("$temppair2")
+ IFS=
+ read i
+ IFS=
+ read i
++ find input_1//
++ egrep '[.]f((ast|)(q|a)|na|sa)(|[.]gz)$'
+ ppinputcheck=0
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-1-501-701_1.fastq.gz = input_1//Le1-1-501-701_1.fastq.gz ']'
+ ppinputcheck=1
+ break
+ '[' 1 = 0 ']'
+ IFS=
+ read i
+ ppinputcheck=0
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-1-501-701_1.fastq.gz = input_1//Le1-1-501-701_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-12-501-708_1.fastq.gz = input_1//Le1-1-501-701_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-17-502-703_1.fastq.gz = input_1//Le1-1-501-701_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-13-502-701_1.fastq.gz = input_1//Le1-1-501-701_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-1-501-701_2.fastq.gz = input_1//Le1-1-501-701_2.fastq.gz ']'
+ ppinputcheck=1
+ break
+ '[' 1 = 0 ']'
+ IFS=
+ read i
+ ppinputcheck=0
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-1-501-701_1.fastq.gz = input_1//Le1-12-501-708_1.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-12-501-708_1.fastq.gz = input_1//Le1-12-501-708_1.fastq.gz ']'
+ ppinputcheck=1
+ break
+ '[' 1 = 0 ']'
+ IFS=
+ read i
+ ppinputcheck=0
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-1-501-701_1.fastq.gz = input_1//Le1-12-501-708_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-12-501-708_1.fastq.gz = input_1//Le1-12-501-708_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-17-502-703_1.fastq.gz = input_1//Le1-12-501-708_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-13-502-701_1.fastq.gz = input_1//Le1-12-501-708_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-1-501-701_2.fastq.gz = input_1//Le1-12-501-708_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-12-501-708_2.fastq.gz = input_1//Le1-12-501-708_2.fastq.gz ']'
+ ppinputcheck=1
+ break
+ '[' 1 = 0 ']'
+ IFS=
+ read i
+ ppinputcheck=0
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-1-501-701_1.fastq.gz = input_1//Le1-17-502-703_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-12-501-708_1.fastq.gz = input_1//Le1-17-502-703_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-17-502-703_1.fastq.gz = input_1//Le1-17-502-703_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-13-502-701_1.fastq.gz = input_1//Le1-17-502-703_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-1-501-701_2.fastq.gz = input_1//Le1-17-502-703_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-12-501-708_2.fastq.gz = input_1//Le1-17-502-703_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-17-502-703_2.fastq.gz = input_1//Le1-17-502-703_2.fastq.gz ']'
+ ppinputcheck=1
+ break
+ '[' 1 = 0 ']'
+ IFS=
+ read i
+ ppinputcheck=0
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-1-501-701_1.fastq.gz = input_1//Le1-13-502-701_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-12-501-708_1.fastq.gz = input_1//Le1-13-502-701_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-17-502-703_1.fastq.gz = input_1//Le1-13-502-701_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-13-502-701_1.fastq.gz = input_1//Le1-13-502-701_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-1-501-701_2.fastq.gz = input_1//Le1-13-502-701_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-12-501-708_2.fastq.gz = input_1//Le1-13-502-701_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-17-502-703_2.fastq.gz = input_1//Le1-13-502-701_2.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-13-502-701_2.fastq.gz = input_1//Le1-13-502-701_2.fastq.gz ']'
+ ppinputcheck=1
+ break
+ '[' 1 = 0 ']'
+ IFS=
+ read i
+ ppinputcheck=0
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-1-501-701_1.fastq.gz = input_1//Le1-17-502-703_1.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-12-501-708_1.fastq.gz = input_1//Le1-17-502-703_1.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-17-502-703_1.fastq.gz = input_1//Le1-17-502-703_1.fastq.gz ']'
+ ppinputcheck=1
+ break
+ '[' 1 = 0 ']'
+ IFS=
+ read i
+ ppinputcheck=0
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-1-501-701_1.fastq.gz = input_1//Le1-13-502-701_1.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-12-501-708_1.fastq.gz = input_1//Le1-13-502-701_1.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-17-502-703_1.fastq.gz = input_1//Le1-13-502-701_1.fastq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1//Le1-13-502-701_1.fastq.gz = input_1//Le1-13-502-701_1.fastq.gz ']'
+ ppinputcheck=1
+ break
+ '[' 1 = 0 ']'
+ IFS=
+ read i
+ mkdir -p output
+ (( i = 0 ))
+ (( i < 4 ))
+ xargs '-d\n' -I '{}' -P 1 bash -c '{}'
++ basename input_1//Le1-1-501-701_1.fastq.gz
+ prefix=output/Le1-1-501-701_1.fastq.gz
+ local_out_files=
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 bbmap.sh ref="input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta" threads="14" in1="input_1//Le1-1-501-701_1.fastq.gz" in2="input_1//Le1-1-501-701_2.fastq.gz" out="output/Le1-1-501-701_1.fastq.gz".temp.bam maxindel=100000 maxsites2=10000 ; PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 bash run-samtools.sh "output/Le1-1-501-701_1.fastq.gz".temp.bam "14" "ON" "6553"'
+ (( i++ ))
+ (( i < 4 ))
++ basename input_1//Le1-12-501-708_1.fastq.gz
+ prefix=output/Le1-12-501-708_1.fastq.gz
+ local_out_files=
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 bbmap.sh ref="input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta" threads="14" in1="input_1//Le1-12-501-708_1.fastq.gz" in2="input_1//Le1-12-501-708_2.fastq.gz" out="output/Le1-12-501-708_1.fastq.gz".temp.bam maxindel=100000 maxsites2=10000 ; PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 bash run-samtools.sh "output/Le1-12-501-708_1.fastq.gz".temp.bam "14" "ON" "6553"'
+ (( i++ ))
+ (( i < 4 ))
++ basename input_1//Le1-17-502-703_1.fastq.gz
+ prefix=output/Le1-17-502-703_1.fastq.gz
+ local_out_files=
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 bbmap.sh ref="input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta" threads="14" in1="input_1//Le1-17-502-703_1.fastq.gz" in2="input_1//Le1-17-502-703_2.fastq.gz" out="output/Le1-17-502-703_1.fastq.gz".temp.bam maxindel=100000 maxsites2=10000 ; PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 bash run-samtools.sh "output/Le1-17-502-703_1.fastq.gz".temp.bam "14" "ON" "6553"'
+ (( i++ ))
+ (( i < 4 ))
++ basename input_1//Le1-13-502-701_1.fastq.gz
+ prefix=output/Le1-13-502-701_1.fastq.gz
+ local_out_files=
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 bbmap.sh ref="input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta" threads="14" in1="input_1//Le1-13-502-701_1.fastq.gz" in2="input_1//Le1-13-502-701_2.fastq.gz" out="output/Le1-13-502-701_1.fastq.gz".temp.bam maxindel=100000 maxsites2=10000 ; PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 bash run-samtools.sh "output/Le1-13-502-701_1.fastq.gz".temp.bam "14" "ON" "6553"'
+ (( i++ ))
+ (( i < 4 ))
java -ea -Xmx109193m -Xms109193m -cp /usr/local/opt/bbmap-38.96-1/current/ align2.BBMap build=1 overwrite=true fastareadlen=500 ref=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta threads=14 in1=input_1//Le1-1-501-701_1.fastq.gz in2=input_1//Le1-1-501-701_2.fastq.gz out=output/Le1-1-501-701_1.fastq.gz.temp.bam maxindel=100000 maxsites2=10000
Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta, threads=14, in1=input_1//Le1-1-501-701_1.fastq.gz, in2=input_1//Le1-1-501-701_2.fastq.gz, out=output/Le1-1-501-701_1.fastq.gz.temp.bam, maxindel=100000, maxsites2=10000]
Version 38.96
Set threads to 14
Retaining first best site only for ambiguous mappings.
NOTE: Ignoring reference file because it already appears to have been processed.
NOTE: If you wish to regenerate the index, please manually delete ref/genome/1/summary.txt
Set genome to 1
Loaded Reference: 0.390 seconds.
Loading index for chunk 1-1, build 1
Generated Index: 1.137 seconds.
Analyzed Index: 3.456 seconds.
Found samtools 1.15
Started output stream: 0.077 seconds.
Cleared Memory: 0.216 seconds.
Processing reads in paired-ended mode.
Started read stream.
Started 14 mapping threads.
Detecting finished threads: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13
------------------ Results ------------------
Genome: 1
Key Length: 13
Max Indel: 100000
Minimum Score Ratio: 0.56
Mapping Mode: normal
Reads Used: 2000000 (302000000 bases)
Mapping: 196.157 seconds.
Reads/sec: 10195.91
kBases/sec: 1539.58
Pairing data: pct pairs num pairs pct bases num bases
mated pairs: 6.0242% 60242 6.0242% 18193084
bad pairs: 0.4714% 4714 0.4714% 1423628
insert size avg: 292.18
Read 1 data: pct reads num reads pct bases num bases
mapped: 6.9196% 69196 6.9196% 10448596
unambiguous: 5.0213% 50213 5.0213% 7582163
ambiguous: 1.8983% 18983 1.8983% 2866433
low-Q discards: 0.0000% 0 0.0000% 0
perfect best site: 3.6137% 36137 3.6137% 5456687
semiperfect site: 3.6238% 36238 3.6238% 5471938
rescued: 0.4217% 4217
Match Rate: NA NA 36.7648% 10022613
Error Rate: 47.7687% 33054 63.2324% 17238085
Sub Rate: 45.2584% 31317 0.9840% 268259
Del Rate: 10.4096% 7203 61.6727% 16812873
Ins Rate: 17.3464% 12003 0.5757% 156953
N Rate: 0.0361% 25 0.0028% 771
Read 2 data: pct reads num reads pct bases num bases
mapped: 6.8722% 68722 6.8722% 10377022
unambiguous: 4.9803% 49803 4.9803% 7520253
ambiguous: 1.8919% 18919 1.8919% 2856769
low-Q discards: 0.0000% 0 0.0000% 0
perfect best site: 3.2269% 32269 3.2269% 4872619
semiperfect site: 3.2366% 32366 3.2366% 4887266
rescued: 0.5981% 5981
Match Rate: NA NA 37.3713% 9913213
Error Rate: 53.0179% 36436 62.6258% 16612276
Sub Rate: 50.7450% 34874 1.1370% 301606
Del Rate: 10.2773% 7063 60.8802% 16149229
Ins Rate: 17.2429% 11850 0.6086% 161441
N Rate: 0.0757% 52 0.0029% 762
Total time: 201.581 seconds.
calulating flagstat...
Sorting and indexing bam
[bam_sort_core] merging from 0 files and 14 in-memory blocks...
Counting mapped reads...
java -ea -Xmx109193m -Xms109193m -cp /usr/local/opt/bbmap-38.96-1/current/ align2.BBMap build=1 overwrite=true fastareadlen=500 ref=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta threads=14 in1=input_1//Le1-12-501-708_1.fastq.gz in2=input_1//Le1-12-501-708_2.fastq.gz out=output/Le1-12-501-708_1.fastq.gz.temp.bam maxindel=100000 maxsites2=10000
Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta, threads=14, in1=input_1//Le1-12-501-708_1.fastq.gz, in2=input_1//Le1-12-501-708_2.fastq.gz, out=output/Le1-12-501-708_1.fastq.gz.temp.bam, maxindel=100000, maxsites2=10000]
Version 38.96
Set threads to 14
Retaining first best site only for ambiguous mappings.
NOTE: Ignoring reference file because it already appears to have been processed.
NOTE: If you wish to regenerate the index, please manually delete ref/genome/1/summary.txt
Set genome to 1
Loaded Reference: 0.376 seconds.
Loading index for chunk 1-1, build 1
Generated Index: 1.131 seconds.
Analyzed Index: 3.415 seconds.
Found samtools 1.15
Started output stream: 0.057 seconds.
Cleared Memory: 0.214 seconds.
Processing reads in paired-ended mode.
Started read stream.
Started 14 mapping threads.
Detecting finished threads: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13
------------------ Results ------------------
Genome: 1
Key Length: 13
Max Indel: 100000
Minimum Score Ratio: 0.56
Mapping Mode: normal
Reads Used: 2000000 (302000000 bases)
Mapping: 58.933 seconds.
Reads/sec: 33936.77
kBases/sec: 5124.45
Pairing data: pct pairs num pairs pct bases num bases
mated pairs: 0.6166% 6166 0.6166% 1862132
bad pairs: 0.0829% 829 0.0829% 250358
insert size avg: 417.26
Read 1 data: pct reads num reads pct bases num bases
mapped: 0.8171% 8171 0.8171% 1233821
unambiguous: 0.5003% 5003 0.5003% 755453
ambiguous: 0.3168% 3168 0.3168% 478368
low-Q discards: 0.0000% 0 0.0000% 0
perfect best site: 0.4606% 4606 0.4606% 695506
semiperfect site: 0.4628% 4628 0.4628% 698828
rescued: 0.0489% 489
Match Rate: NA NA 15.3850% 1187753
Error Rate: 43.6299% 3565 84.6150% 6532460
Sub Rate: 38.7590% 3167 0.3571% 27571
Del Rate: 10.8799% 889 84.0183% 6486393
Ins Rate: 18.6146% 1521 0.2396% 18496
N Rate: 0.0122% 1 0.0000% 1
Read 2 data: pct reads num reads pct bases num bases
mapped: 0.8057% 8057 0.8057% 1216607
unambiguous: 0.4938% 4938 0.4938% 745638
ambiguous: 0.3119% 3119 0.3119% 470969
low-Q discards: 0.0000% 0 0.0000% 0
perfect best site: 0.4006% 4006 0.4006% 604906
semiperfect site: 0.4035% 4035 0.4035% 609285
rescued: 0.0759% 759
Match Rate: NA NA 17.3427% 1166567
Error Rate: 50.2668% 4050 82.6568% 5559955
Sub Rate: 46.2083% 3723 0.4822% 32433
Del Rate: 10.6739% 860 81.9134% 5509951
Ins Rate: 17.4755% 1408 0.2612% 17571
N Rate: 0.0621% 5 0.0005% 36
Total time: 64.253 seconds.
calulating flagstat...
Sorting and indexing bam
[bam_sort_core] merging from 0 files and 14 in-memory blocks...
Counting mapped reads...
java -ea -Xmx109181m -Xms109181m -cp /usr/local/opt/bbmap-38.96-1/current/ align2.BBMap build=1 overwrite=true fastareadlen=500 ref=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta threads=14 in1=input_1//Le1-17-502-703_1.fastq.gz in2=input_1//Le1-17-502-703_2.fastq.gz out=output/Le1-17-502-703_1.fastq.gz.temp.bam maxindel=100000 maxsites2=10000
Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta, threads=14, in1=input_1//Le1-17-502-703_1.fastq.gz, in2=input_1//Le1-17-502-703_2.fastq.gz, out=output/Le1-17-502-703_1.fastq.gz.temp.bam, maxindel=100000, maxsites2=10000]
Version 38.96
Set threads to 14
Retaining first best site only for ambiguous mappings.
NOTE: Ignoring reference file because it already appears to have been processed.
NOTE: If you wish to regenerate the index, please manually delete ref/genome/1/summary.txt
Set genome to 1
Loaded Reference: 0.373 seconds.
Loading index for chunk 1-1, build 1
Generated Index: 1.079 seconds.
Analyzed Index: 3.421 seconds.
Found samtools 1.15
Started output stream: 0.072 seconds.
Cleared Memory: 0.188 seconds.
Processing reads in paired-ended mode.
Started read stream.
Started 14 mapping threads.
Detecting finished threads: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13
------------------ Results ------------------
Genome: 1
Key Length: 13
Max Indel: 100000
Minimum Score Ratio: 0.56
Mapping Mode: normal
Reads Used: 2000000 (302000000 bases)
Mapping: 807.637 seconds.
Reads/sec: 2476.36
kBases/sec: 373.93
Pairing data: pct pairs num pairs pct bases num bases
mated pairs: 28.3931% 283931 28.3931% 85747162
bad pairs: 2.5956% 25956 2.5956% 7838712
insert size avg: 339.04
Read 1 data: pct reads num reads pct bases num bases
mapped: 32.5483% 325483 32.5483% 49147933
unambiguous: 21.6019% 216019 21.6019% 32618869
ambiguous: 10.9464% 109464 10.9464% 16529064
low-Q discards: 0.0000% 0 0.0000% 0
perfect best site: 20.6655% 206655 20.6655% 31204905
semiperfect site: 20.7156% 207156 20.7156% 31280556
rescued: 1.7673% 17673
Match Rate: NA NA 31.7415% 48059882
Error Rate: 36.4949% 118786 68.2563% 103347167
Sub Rate: 34.2766% 111566 0.4938% 747709
Del Rate: 7.8980% 25707 67.5399% 102262431
Ins Rate: 9.4446% 30741 0.2226% 337027
N Rate: 0.0418% 136 0.0022% 3315
Read 2 data: pct reads num reads pct bases num bases
mapped: 32.2561% 322561 32.2561% 48706711
unambiguous: 21.3931% 213931 21.3931% 32303581
ambiguous: 10.8630% 108630 10.8630% 16403130
low-Q discards: 0.0000% 0 0.0000% 0
perfect best site: 17.8848% 178848 17.8848% 27006048
semiperfect site: 17.9266% 179266 17.9266% 27069166
rescued: 2.1757% 21757
Match Rate: NA NA 32.4895% 47428610
Error Rate: 44.5292% 143636 67.5075% 98548430
Sub Rate: 42.5829% 137358 0.6448% 941299
Del Rate: 7.7231% 24912 66.6350% 97274658
Ins Rate: 9.4052% 30338 0.2278% 332473
N Rate: 0.0741% 239 0.0030% 4329
Total time: 812.905 seconds.
calulating flagstat...
Sorting and indexing bam
[bam_sort_core] merging from 0 files and 14 in-memory blocks...
Counting mapped reads...
java -ea -Xmx109194m -Xms109194m -cp /usr/local/opt/bbmap-38.96-1/current/ align2.BBMap build=1 overwrite=true fastareadlen=500 ref=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta threads=14 in1=input_1//Le1-13-502-701_1.fastq.gz in2=input_1//Le1-13-502-701_2.fastq.gz out=output/Le1-13-502-701_1.fastq.gz.temp.bam maxindel=100000 maxsites2=10000
Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta, threads=14, in1=input_1//Le1-13-502-701_1.fastq.gz, in2=input_1//Le1-13-502-701_2.fastq.gz, out=output/Le1-13-502-701_1.fastq.gz.temp.bam, maxindel=100000, maxsites2=10000]
Version 38.96
Set threads to 14
Retaining first best site only for ambiguous mappings.
NOTE: Ignoring reference file because it already appears to have been processed.
NOTE: If you wish to regenerate the index, please manually delete ref/genome/1/summary.txt
Set genome to 1
Loaded Reference: 0.382 seconds.
Loading index for chunk 1-1, build 1
Generated Index: 1.153 seconds.
Analyzed Index: 3.522 seconds.
Found samtools 1.15
Started output stream: 0.066 seconds.
Cleared Memory: 0.195 seconds.
Processing reads in paired-ended mode.
Started read stream.
Started 14 mapping threads.
Detecting finished threads: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13
------------------ Results ------------------
Genome: 1
Key Length: 13
Max Indel: 100000
Minimum Score Ratio: 0.56
Mapping Mode: normal
Reads Used: 2000000 (302000000 bases)
Mapping: 250.440 seconds.
Reads/sec: 7985.95
kBases/sec: 1205.88
Pairing data: pct pairs num pairs pct bases num bases
mated pairs: 10.0927% 100927 10.0927% 30479954
bad pairs: 0.8867% 8867 0.8867% 2677834
insert size avg: 381.70
Read 1 data: pct reads num reads pct bases num bases
mapped: 11.6839% 116839 11.6839% 17642689
unambiguous: 8.1950% 81950 8.1950% 12374450
ambiguous: 3.4889% 34889 3.4889% 5268239
low-Q discards: 0.0000% 0 0.0000% 0
perfect best site: 7.5404% 75404 7.5404% 11386004
semiperfect site: 7.5537% 75537 7.5537% 11406087
rescued: 0.6799% 6799
Match Rate: NA NA 33.2878% 17247522
Error Rate: 35.4462% 41415 66.7094% 34564390
Sub Rate: 32.7006% 38207 0.4974% 257723
Del Rate: 7.6969% 8993 65.9495% 34170663
Ins Rate: 10.3048% 12040 0.2625% 136004
N Rate: 0.0462% 54 0.0028% 1440
Read 2 data: pct reads num reads pct bases num bases
mapped: 11.5805% 115805 11.5805% 17486555
unambiguous: 8.1197% 81197 8.1197% 12260747
ambiguous: 3.4608% 34608 3.4608% 5225808
low-Q discards: 0.0000% 0 0.0000% 0
perfect best site: 6.2792% 62792 6.2792% 9481592
semiperfect site: 6.2914% 62914 6.2914% 9500014
rescued: 0.8684% 8684
Match Rate: NA NA 34.6408% 17006518
Error Rate: 45.7507% 52982 65.3551% 32085334
Sub Rate: 43.3466% 50198 0.6998% 343567
Del Rate: 7.5782% 8776 64.3814% 31607304
Ins Rate: 10.1117% 11710 0.2739% 134463
N Rate: 0.0786% 91 0.0041% 2007
Total time: 255.895 seconds.
calulating flagstat...
Sorting and indexing bam
[bam_sort_core] merging from 0 files and 14 in-memory blocks...
Counting mapped reads...
++ date
+ echo completion at Wed Mar 1 02:20:44 JST 2023
completion at Wed Mar 1 02:20:44 JST 2023
++ date +%s
+ time_fin=1677604844
++ echo 'scale=2; (1677604844 - 1677603491)/60'
++ bc
+ echo -e 'Total running time is 22.55 min'
Total running time is 22.55 min
+ echo 'Run completed!'
Run completed!
+ post_processing
+ '[' 2 = 1 ']'
+ exit
++ echo input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
+ ref=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
++ echo input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
++ sed 's/[.]\(fa\|fasta\|fsa\|fna\)$//'
+ refbase=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg
+ FUNC_RUN_DOCKER quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools faidx input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
+ PP_RUN_IMAGE=quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230301_022044_781_15034
+ echo pp20230301_022044_781_15034
++ id -u
++ id -g
+ docker run --name pp20230301_022044_781_15034 -v /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants:/yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants -w /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools faidx input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
+ FUNC_RUN_DOCKER quay.io/biocontainers/picard:2.18.27--0 picard -Xmx104857M CreateSequenceDictionary R=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta O=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.dict
+ PP_RUN_IMAGE=quay.io/biocontainers/picard:2.18.27--0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230301_022045_717_10950
+ echo pp20230301_022045_717_10950
++ id -u
++ id -g
+ docker run --name pp20230301_022045_717_10950 -v /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants:/yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants -w /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants -u 2007:600 -i --rm quay.io/biocontainers/picard:2.18.27--0 picard -Xmx104857M CreateSequenceDictionary R=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta O=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.dict
/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
INFO 2023-02-28 17:20:46 CreateSequenceDictionary
********** NOTE: Picard's command line syntax is changing.
**********
********** For more information, please see:
********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
**********
********** The command line looks like this in the new syntax:
**********
********** CreateSequenceDictionary -R input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta -O input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.dict
**********
17:20:47.401 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/picard-2.18.27-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Tue Feb 28 17:20:47 GMT 2023] CreateSequenceDictionary OUTPUT=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.dict REFERENCE=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Tue Feb 28 17:20:47 GMT 2023] Executing as ?@49b6953b65e9 on Linux 3.10.0-1160.36.2.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.27-SNAPSHOT
[Tue Feb 28 17:20:47 GMT 2023] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2147483648
+ cat
+ mkdir -p output.temp output2
+ read i
+ xargs '-d\n' -I '{}' -P 1 bash -c '{}'
+ ls output/Le1-1-501-701_1.fastq.gz.bam output/Le1-12-501-708_1.fastq.gz.bam output/Le1-13-502-701_1.fastq.gz.bam output/Le1-17-502-703_1.fastq.gz.bam
++ basenmae output/Le1-1-501-701_1.fastq.gz.bam .bam
/yoshitake/PortablePipeline/PortablePipeline/scripts/RNA-seq~SNPcall-bbmap-callvariants: 行 56: basenmae: コマンドが見つかりません
+ j=
++ onerror 61
++ status=1
++ script=/yoshitake/PortablePipeline/PortablePipeline/scripts/RNA-seq~SNPcall-bbmap-callvariants
++ line=61
++ shift
++ set +x
------------------------------------------------------------
Error occured on /yoshitake/PortablePipeline/PortablePipeline/scripts/RNA-seq~SNPcall-bbmap-callvariants [Line 61]: Status 1
PID: 348967
User: yoshitake.kazutoshi
Current directory: /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants
Command line: /yoshitake/PortablePipeline/PortablePipeline/scripts/RNA-seq~SNPcall-bbmap-callvariants
------------------------------------------------------------
PID: 348965
pp runtime error.
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-1-501-701_1.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-1-501-701_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-12-501-708_1.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-12-501-708_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-17-502-703_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-13-502-701_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-17-502-703_1.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-13-502-701_1.fastq.gz
0 input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
script: /yoshitake/PortablePipeline/PortablePipeline/scripts/RNA-seq~SNPcall-bbmap-callvariants "$scriptdir"/mapping-illumina~bbmap
broadinstitute/gatk:4.3.0.0 centos:centos6 quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 quay.io/biocontainers/picard:2.18.27--0
using docker
+ set -o pipefail
++ date +%s
+ time0=1677627175
+ echo start at 1677627175
start at 1677627175
++ echo input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
+ ref=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
++ echo input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
++ sed 's/[.]\(fa\|fasta\|fsa\|fna\)$//'
+ refbase=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg
+ FUNC_RUN_DOCKER quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools faidx input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
+ PP_RUN_IMAGE=quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230301_083255_301_249
+ echo pp20230301_083255_301_249
++ id -u
++ id -g
+ docker run --name pp20230301_083255_301_249 -v /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants:/yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants -w /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools faidx input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
+ FUNC_RUN_DOCKER quay.io/biocontainers/picard:2.18.27--0 picard -Xmx104857M CreateSequenceDictionary R=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta O=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.dict
+ PP_RUN_IMAGE=quay.io/biocontainers/picard:2.18.27--0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230301_083256_208_845
+ echo pp20230301_083256_208_845
++ id -u
++ id -g
+ docker run --name pp20230301_083256_208_845 -v /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants:/yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants -w /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants -u 2007:600 -i --rm quay.io/biocontainers/picard:2.18.27--0 picard -Xmx104857M CreateSequenceDictionary R=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta O=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.dict
/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
INFO 2023-02-28 23:32:57 CreateSequenceDictionary
********** NOTE: Picard's command line syntax is changing.
**********
********** For more information, please see:
********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
**********
********** The command line looks like this in the new syntax:
**********
********** CreateSequenceDictionary -R input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta -O input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.dict
**********
23:32:57.543 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/picard-2.18.27-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Tue Feb 28 23:32:57 GMT 2023] CreateSequenceDictionary OUTPUT=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.dict REFERENCE=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Tue Feb 28 23:32:57 GMT 2023] Executing as ?@02a181fd478b on Linux 3.10.0-1160.36.2.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.27-SNAPSHOT
[Tue Feb 28 23:32:57 GMT 2023] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2147483648
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" picard.PicardException: /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.dict already exists. Delete this file and try again, or specify a different output file.
at picard.sam.CreateSequenceDictionary.doWork(CreateSequenceDictionary.java:209)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:295)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)
PID: 403851
pp runtime error.
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-1-501-701_1.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-1-501-701_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-12-501-708_1.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-12-501-708_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-17-502-703_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-13-502-701_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-17-502-703_1.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-13-502-701_1.fastq.gz
0 input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
script: /yoshitake/PortablePipeline/PortablePipeline/scripts/RNA-seq~SNPcall-bbmap-callvariants "$scriptdir"/mapping-illumina~bbmap
broadinstitute/gatk:4.3.0.0 centos:centos6 quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 quay.io/biocontainers/picard:2.18.27--0
using docker
+ set -o pipefail
++ date +%s
+ time0=1677627548
+ echo start at 1677627548
start at 1677627548
++ echo input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
+ ref=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
++ echo input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
++ sed 's/[.]\(fa\|fasta\|fsa\|fna\)$//'
+ refbase=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg
+ FUNC_RUN_DOCKER quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools faidx input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
+ PP_RUN_IMAGE=quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230301_083908_407_13623
+ echo pp20230301_083908_407_13623
++ id -u
++ id -g
+ docker run --name pp20230301_083908_407_13623 -v /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants:/yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants -w /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools faidx input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
+ rm -f input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.dict
+ FUNC_RUN_DOCKER quay.io/biocontainers/picard:2.18.27--0 picard -Xmx104857M CreateSequenceDictionary R=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta O=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.dict
+ PP_RUN_IMAGE=quay.io/biocontainers/picard:2.18.27--0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230301_083909_334_23984
+ echo pp20230301_083909_334_23984
++ id -u
++ id -g
+ docker run --name pp20230301_083909_334_23984 -v /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants:/yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants -w /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants -u 2007:600 -i --rm quay.io/biocontainers/picard:2.18.27--0 picard -Xmx104857M CreateSequenceDictionary R=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta O=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.dict
/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
INFO 2023-02-28 23:39:10 CreateSequenceDictionary
********** NOTE: Picard's command line syntax is changing.
**********
********** For more information, please see:
********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
**********
********** The command line looks like this in the new syntax:
**********
********** CreateSequenceDictionary -R input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta -O input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.dict
**********
23:39:10.680 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/picard-2.18.27-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Tue Feb 28 23:39:10 GMT 2023] CreateSequenceDictionary OUTPUT=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.dict REFERENCE=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Tue Feb 28 23:39:10 GMT 2023] Executing as ?@dfee3dc54eee on Linux 3.10.0-1160.36.2.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.27-SNAPSHOT
[Tue Feb 28 23:39:11 GMT 2023] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2147483648
+ cat
+ mkdir -p output.temp output2
+ read i
+ xargs '-d\n' -I '{}' -P 1 bash -c '{}'
+ ls output/Le1-1-501-701_1.fastq.gz.bam output/Le1-12-501-708_1.fastq.gz.bam output/Le1-13-502-701_1.fastq.gz.bam output/Le1-17-502-703_1.fastq.gz.bam
++ basename output/Le1-1-501-701_1.fastq.gz.bam .bam
+ j=Le1-1-501-701_1.fastq.gz
+ echo -n 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/picard:2.18.27--0 picard -Xmx104857M AddOrReplaceReadGroups I="output/Le1-1-501-701_1.fastq.gz.bam" O=output.temp/"Le1-1-501-701_1.fastq.gz"_addrg.bam SO=coordinate RGID="Le1-1-501-701_1.fastq.gz" RGLB=library RGPL=Illumina RGPU=Illumina RGSM="Le1-1-501-701_1.fastq.gz"; '
+ echo -n '(PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools view -h output.temp/"Le1-1-501-701_1.fastq.gz"_addrg.bam)|bash run-awk-replace.sh|(PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools view -Sb -o output.temp/"Le1-1-501-701_1.fastq.gz"_addrg_repN.bam; '
+ echo -n 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools index output.temp/"Le1-1-501-701_1.fastq.gz"_addrg_repN.bam; '
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm broadinstitute/gatk:4.3.0.0 gatk -Xmx104857M SplitNCigarReads -R "input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta" -I output.temp/"Le1-1-501-701_1.fastq.gz"_addrg_repN.bam -O output2/"Le1-1-501-701_1.fastq.gz".bam'
+ read i
++ basename output/Le1-12-501-708_1.fastq.gz.bam .bam
+ j=Le1-12-501-708_1.fastq.gz
+ echo -n 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/picard:2.18.27--0 picard -Xmx104857M AddOrReplaceReadGroups I="output/Le1-12-501-708_1.fastq.gz.bam" O=output.temp/"Le1-12-501-708_1.fastq.gz"_addrg.bam SO=coordinate RGID="Le1-12-501-708_1.fastq.gz" RGLB=library RGPL=Illumina RGPU=Illumina RGSM="Le1-12-501-708_1.fastq.gz"; '
+ echo -n '(PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools view -h output.temp/"Le1-12-501-708_1.fastq.gz"_addrg.bam)|bash run-awk-replace.sh|(PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools view -Sb -o output.temp/"Le1-12-501-708_1.fastq.gz"_addrg_repN.bam; '
+ echo -n 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools index output.temp/"Le1-12-501-708_1.fastq.gz"_addrg_repN.bam; '
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm broadinstitute/gatk:4.3.0.0 gatk -Xmx104857M SplitNCigarReads -R "input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta" -I output.temp/"Le1-12-501-708_1.fastq.gz"_addrg_repN.bam -O output2/"Le1-12-501-708_1.fastq.gz".bam'
+ read i
++ basename output/Le1-13-502-701_1.fastq.gz.bam .bam
bash: -c: 行 1: 構文エラー: 予期しないファイル終了 (EOF) です
+ j=Le1-13-502-701_1.fastq.gz
+ echo -n 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/picard:2.18.27--0 picard -Xmx104857M AddOrReplaceReadGroups I="output/Le1-13-502-701_1.fastq.gz.bam" O=output.temp/"Le1-13-502-701_1.fastq.gz"_addrg.bam SO=coordinate RGID="Le1-13-502-701_1.fastq.gz" RGLB=library RGPL=Illumina RGPU=Illumina RGSM="Le1-13-502-701_1.fastq.gz"; '
+ echo -n '(PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools view -h output.temp/"Le1-13-502-701_1.fastq.gz"_addrg.bam)|bash run-awk-replace.sh|(PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools view -Sb -o output.temp/"Le1-13-502-701_1.fastq.gz"_addrg_repN.bam; '
+ echo -n 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools index output.temp/"Le1-13-502-701_1.fastq.gz"_addrg_repN.bam; '
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm broadinstitute/gatk:4.3.0.0 gatk -Xmx104857M SplitNCigarReads -R "input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta" -I output.temp/"Le1-13-502-701_1.fastq.gz"_addrg_repN.bam -O output2/"Le1-13-502-701_1.fastq.gz".bam'
+ read i
++ basename output/Le1-17-502-703_1.fastq.gz.bam .bam
bash: -c: 行 1: 構文エラー: 予期しないファイル終了 (EOF) です
+ j=Le1-17-502-703_1.fastq.gz
+ echo -n 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/picard:2.18.27--0 picard -Xmx104857M AddOrReplaceReadGroups I="output/Le1-17-502-703_1.fastq.gz.bam" O=output.temp/"Le1-17-502-703_1.fastq.gz"_addrg.bam SO=coordinate RGID="Le1-17-502-703_1.fastq.gz" RGLB=library RGPL=Illumina RGPU=Illumina RGSM="Le1-17-502-703_1.fastq.gz"; '
+ echo -n '(PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools view -h output.temp/"Le1-17-502-703_1.fastq.gz"_addrg.bam)|bash run-awk-replace.sh|(PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools view -Sb -o output.temp/"Le1-17-502-703_1.fastq.gz"_addrg_repN.bam; '
+ echo -n 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools index output.temp/"Le1-17-502-703_1.fastq.gz"_addrg_repN.bam; '
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm broadinstitute/gatk:4.3.0.0 gatk -Xmx104857M SplitNCigarReads -R "input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta" -I output.temp/"Le1-17-502-703_1.fastq.gz"_addrg_repN.bam -O output2/"Le1-17-502-703_1.fastq.gz".bam'
+ read i
bash: -c: 行 1: 構文エラー: 予期しないファイル終了 (EOF) です
bash: -c: 行 1: 構文エラー: 予期しないファイル終了 (EOF) です
++ onerror 62
++ status=123
++ script=/yoshitake/PortablePipeline/PortablePipeline/scripts/RNA-seq~SNPcall-bbmap-callvariants
++ line=62
++ shift
++ set +x
------------------------------------------------------------
Error occured on /yoshitake/PortablePipeline/PortablePipeline/scripts/RNA-seq~SNPcall-bbmap-callvariants [Line 62]: Status 123
PID: 405362
User: yoshitake.kazutoshi
Current directory: /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants
Command line: /yoshitake/PortablePipeline/PortablePipeline/scripts/RNA-seq~SNPcall-bbmap-callvariants
------------------------------------------------------------
PID: 405360
pp runtime error.
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-1-501-701_1.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-1-501-701_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-12-501-708_1.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-12-501-708_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-17-502-703_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-13-502-701_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-17-502-703_1.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-13-502-701_1.fastq.gz
0 input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
script: /yoshitake/PortablePipeline/PortablePipeline/scripts/RNA-seq~SNPcall-bbmap-callvariants "$scriptdir"/mapping-illumina~bbmap
broadinstitute/gatk:4.3.0.0 centos:centos6 quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 quay.io/biocontainers/picard:2.18.27--0
using docker
+ set -o pipefail
++ date +%s
+ time0=1677627617
+ echo start at 1677627617
start at 1677627617
++ echo input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
+ ref=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
++ echo input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
++ sed 's/[.]\(fa\|fasta\|fsa\|fna\)$//'
+ refbase=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg
+ FUNC_RUN_DOCKER quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools faidx input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
+ PP_RUN_IMAGE=quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230301_084017_338_885
+ echo pp20230301_084017_338_885
++ id -u
++ id -g
+ docker run --name pp20230301_084017_338_885 -v /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants:/yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants -w /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools faidx input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
+ rm -f input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.dict
+ FUNC_RUN_DOCKER quay.io/biocontainers/picard:2.18.27--0 picard -Xmx104857M CreateSequenceDictionary R=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta O=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.dict
+ PP_RUN_IMAGE=quay.io/biocontainers/picard:2.18.27--0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230301_084018_231_32683
+ echo pp20230301_084018_231_32683
++ id -u
++ id -g
+ docker run --name pp20230301_084018_231_32683 -v /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants:/yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants -w /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants -u 2007:600 -i --rm quay.io/biocontainers/picard:2.18.27--0 picard -Xmx104857M CreateSequenceDictionary R=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta O=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.dict
/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
INFO 2023-02-28 23:40:19 CreateSequenceDictionary
********** NOTE: Picard's command line syntax is changing.
**********
********** For more information, please see:
********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
**********
********** The command line looks like this in the new syntax:
**********
********** CreateSequenceDictionary -R input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta -O input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.dict
**********
23:40:20.001 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/picard-2.18.27-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Tue Feb 28 23:40:20 GMT 2023] CreateSequenceDictionary OUTPUT=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.dict REFERENCE=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Tue Feb 28 23:40:20 GMT 2023] Executing as ?@a530dca5357e on Linux 3.10.0-1160.36.2.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.27-SNAPSHOT
[Tue Feb 28 23:40:20 GMT 2023] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2147483648
+ cat
+ mkdir -p output.temp output2
+ ls output/Le1-1-501-701_1.fastq.gz.bam output/Le1-12-501-708_1.fastq.gz.bam output/Le1-13-502-701_1.fastq.gz.bam output/Le1-17-502-703_1.fastq.gz.bam
+ read i
+ xargs '-d\n' -I '{}' -P 1 bash -c '{}'
++ basename output/Le1-1-501-701_1.fastq.gz.bam .bam
+ j=Le1-1-501-701_1.fastq.gz
+ echo -n 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/picard:2.18.27--0 picard -Xmx104857M AddOrReplaceReadGroups I="output/Le1-1-501-701_1.fastq.gz.bam" O=output.temp/"Le1-1-501-701_1.fastq.gz"_addrg.bam SO=coordinate RGID="Le1-1-501-701_1.fastq.gz" RGLB=library RGPL=Illumina RGPU=Illumina RGSM="Le1-1-501-701_1.fastq.gz"; '
+ echo -n '(PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools view -h output.temp/"Le1-1-501-701_1.fastq.gz"_addrg.bam)|bash run-awk-replace.sh|(PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools view -Sb -o output.temp/"Le1-1-501-701_1.fastq.gz"_addrg_repN.bam); '
+ echo -n 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools index output.temp/"Le1-1-501-701_1.fastq.gz"_addrg_repN.bam; '
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm broadinstitute/gatk:4.3.0.0 gatk -Xmx104857M SplitNCigarReads -R "input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta" -I output.temp/"Le1-1-501-701_1.fastq.gz"_addrg_repN.bam -O output2/"Le1-1-501-701_1.fastq.gz".bam'
+ read i
++ basename output/Le1-12-501-708_1.fastq.gz.bam .bam
+ j=Le1-12-501-708_1.fastq.gz
+ echo -n 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/picard:2.18.27--0 picard -Xmx104857M AddOrReplaceReadGroups I="output/Le1-12-501-708_1.fastq.gz.bam" O=output.temp/"Le1-12-501-708_1.fastq.gz"_addrg.bam SO=coordinate RGID="Le1-12-501-708_1.fastq.gz" RGLB=library RGPL=Illumina RGPU=Illumina RGSM="Le1-12-501-708_1.fastq.gz"; '
+ echo -n '(PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools view -h output.temp/"Le1-12-501-708_1.fastq.gz"_addrg.bam)|bash run-awk-replace.sh|(PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools view -Sb -o output.temp/"Le1-12-501-708_1.fastq.gz"_addrg_repN.bam); '
+ echo -n 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools index output.temp/"Le1-12-501-708_1.fastq.gz"_addrg_repN.bam; '
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm broadinstitute/gatk:4.3.0.0 gatk -Xmx104857M SplitNCigarReads -R "input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta" -I output.temp/"Le1-12-501-708_1.fastq.gz"_addrg_repN.bam -O output2/"Le1-12-501-708_1.fastq.gz".bam'
+ read i
++ basename output/Le1-13-502-701_1.fastq.gz.bam .bam
+ j=Le1-13-502-701_1.fastq.gz
+ echo -n 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/picard:2.18.27--0 picard -Xmx104857M AddOrReplaceReadGroups I="output/Le1-13-502-701_1.fastq.gz.bam" O=output.temp/"Le1-13-502-701_1.fastq.gz"_addrg.bam SO=coordinate RGID="Le1-13-502-701_1.fastq.gz" RGLB=library RGPL=Illumina RGPU=Illumina RGSM="Le1-13-502-701_1.fastq.gz"; '
+ echo -n '(PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools view -h output.temp/"Le1-13-502-701_1.fastq.gz"_addrg.bam)|bash run-awk-replace.sh|(PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools view -Sb -o output.temp/"Le1-13-502-701_1.fastq.gz"_addrg_repN.bam); '
+ echo -n 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools index output.temp/"Le1-13-502-701_1.fastq.gz"_addrg_repN.bam; '
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm broadinstitute/gatk:4.3.0.0 gatk -Xmx104857M SplitNCigarReads -R "input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta" -I output.temp/"Le1-13-502-701_1.fastq.gz"_addrg_repN.bam -O output2/"Le1-13-502-701_1.fastq.gz".bam'
+ read i
++ basename output/Le1-17-502-703_1.fastq.gz.bam .bam
+ j=Le1-17-502-703_1.fastq.gz
+ echo -n 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/picard:2.18.27--0 picard -Xmx104857M AddOrReplaceReadGroups I="output/Le1-17-502-703_1.fastq.gz.bam" O=output.temp/"Le1-17-502-703_1.fastq.gz"_addrg.bam SO=coordinate RGID="Le1-17-502-703_1.fastq.gz" RGLB=library RGPL=Illumina RGPU=Illumina RGSM="Le1-17-502-703_1.fastq.gz"; '
+ echo -n '(PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools view -h output.temp/"Le1-17-502-703_1.fastq.gz"_addrg.bam)|bash run-awk-replace.sh|(PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools view -Sb -o output.temp/"Le1-17-502-703_1.fastq.gz"_addrg_repN.bam); '
+ echo -n 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools index output.temp/"Le1-17-502-703_1.fastq.gz"_addrg_repN.bam; '
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm broadinstitute/gatk:4.3.0.0 gatk -Xmx104857M SplitNCigarReads -R "input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta" -I output.temp/"Le1-17-502-703_1.fastq.gz"_addrg_repN.bam -O output2/"Le1-17-502-703_1.fastq.gz".bam'
+ read i
/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
INFO 2023-02-28 23:40:21 AddOrReplaceReadGroups
********** NOTE: Picard's command line syntax is changing.
**********
********** For more information, please see:
********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
**********
********** The command line looks like this in the new syntax:
**********
********** AddOrReplaceReadGroups -I output/Le1-1-501-701_1.fastq.gz.bam -O output.temp/Le1-1-501-701_1.fastq.gz_addrg.bam -SO coordinate -RGID Le1-1-501-701_1.fastq.gz -RGLB library -RGPL Illumina -RGPU Illumina -RGSM Le1-1-501-701_1.fastq.gz
**********
23:40:22.113 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/picard-2.18.27-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Tue Feb 28 23:40:22 GMT 2023] AddOrReplaceReadGroups INPUT=output/Le1-1-501-701_1.fastq.gz.bam OUTPUT=output.temp/Le1-1-501-701_1.fastq.gz_addrg.bam SORT_ORDER=coordinate RGID=Le1-1-501-701_1.fastq.gz RGLB=library RGPL=Illumina RGPU=Illumina RGSM=Le1-1-501-701_1.fastq.gz VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Tue Feb 28 23:40:22 GMT 2023] Executing as ?@1869a7c02967 on Linux 3.10.0-1160.36.2.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.27-SNAPSHOT
INFO 2023-02-28 23:40:22 AddOrReplaceReadGroups Created read-group ID=Le1-1-501-701_1.fastq.gz PL=Illumina LB=library SM=Le1-1-501-701_1.fastq.gz
[Tue Feb 28 23:40:25 GMT 2023] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2583691264
[1m[31mUSAGE: [32m[1m[31m [-h]
[0m[1m[31mAvailable Programs:
[0m[37m--------------------------------------------------------------------------------------
[0m[31mBase Calling: Tools that process sequencing machine data, e.g. Illumina base calls, and detect sequencing level attributes, e.g. adapters[0m
[32m CheckIlluminaDirectory (Picard) [36mAsserts the validity for specified Illumina basecalling data. [0m
[32m CollectIlluminaBasecallingMetrics (Picard) [36mCollects Illumina Basecalling metrics for a sequencing run. [0m
[32m CollectIlluminaLaneMetrics (Picard) [36mCollects Illumina lane metrics for the given BaseCalling analysis directory.[0m
[32m ExtractIlluminaBarcodes (Picard) [36mTool determines the barcode for each read in an Illumina lane. [0m
[32m IlluminaBasecallsToFastq (Picard) [36mGenerate FASTQ file(s) from Illumina basecall read data. [0m
[32m IlluminaBasecallsToSam (Picard) [36mTransforms raw Illumina sequencing data into an unmapped SAM, BAM or CRAM file.[0m
[32m MarkIlluminaAdapters (Picard) [36mReads a SAM/BAM/CRAM file and rewrites it with new adapter-trimming tags. [0m
[37m--------------------------------------------------------------------------------------
[0m[31mCopy Number Variant Discovery: Tools that analyze read coverage to detect copy number variants.[0m
[32m AnnotateIntervals [36mAnnotates intervals with GC content, mappability, and segmental-duplication content[0m
[32m CallCopyRatioSegments [36mCalls copy-ratio segments as amplified, deleted, or copy-number neutral[0m
[32m CombineSegmentBreakpoints [31m(EXPERIMENTAL Tool) [36mCombine the breakpoints of two segment files and annotate the resulting intervals with chosen columns from each file.[0m
[32m CreateReadCountPanelOfNormals [36mCreates a panel of normals for read-count denoising[0m
[32m DenoiseReadCounts [36mDenoises read counts to produce denoised copy ratios[0m
[32m DetermineGermlineContigPloidy [36mDetermines the baseline contig ploidy for germline samples given counts data[0m
[32m FilterIntervals [36mFilters intervals based on annotations and/or count statistics[0m
[32m GermlineCNVCaller [36mCalls copy-number variants in germline samples given their counts and the output of DetermineGermlineContigPloidy[0m
[32m MergeAnnotatedRegions [31m(EXPERIMENTAL Tool) [36mMerge annotated genomic regions based entirely on touching/overlapping intervals.[0m
[32m MergeAnnotatedRegionsByAnnotation [31m(EXPERIMENTAL Tool) [36mMerge annotated genomic regions within specified distance if annotation value(s) are exactly the same.[0m
[32m ModelSegments [36mModels segmented copy ratios from denoised copy ratios and segmented minor-allele fractions from allelic counts[0m
[32m PlotDenoisedCopyRatios [36mCreates plots of denoised copy ratios[0m
[32m PlotModeledSegments [36mCreates plots of denoised and segmented copy-ratio and minor-allele-fraction estimates[0m
[32m PostprocessGermlineCNVCalls [36mPostprocesses the output of GermlineCNVCaller and generates VCFs and denoised copy ratios[0m
[32m TagGermlineEvents [31m(EXPERIMENTAL Tool) [36mDo a simplistic tagging of germline events in a tumor segment file.[0m
[37m--------------------------------------------------------------------------------------
[0m[31mCoverage Analysis: Tools that count coverage, e.g. depth per allele[0m
[32m ASEReadCounter [36mGenerates table of filtered base counts at het sites for allele specific expression[0m
[32m AnalyzeSaturationMutagenesis [31m(BETA Tool) [36m(EXPERIMENTAL) Processes reads from a MITESeq or other saturation mutagenesis experiment.[0m
[32m CollectAllelicCounts [36mCollects reference and alternate allele counts at specified sites[0m
[32m CollectAllelicCountsSpark [36mCollects reference and alternate allele counts at specified sites[0m
[32m CollectF1R2Counts [36mCollect F1R2 read counts for the Mutect2 orientation bias mixture model filter[0m
[32m CollectReadCounts [36mCollects read counts at specified intervals[0m
[32m CountBases [36mCount bases in a SAM/BAM/CRAM file[0m
[32m CountBasesSpark [36mCounts bases in the input SAM/BAM[0m
[32m CountReads [36mCount reads in a SAM/BAM/CRAM file[0m
[32m CountReadsSpark [36mCounts reads in the input SAM/BAM[0m
[32m DepthOfCoverage [31m(BETA Tool) [36mGenerate coverage summary information for reads data[0m
[32m GatherNormalArtifactData [36mCombine output files from GetNormalArtifactData in the order defined by a sequence dictionary[0m
[32m GeneExpressionEvaluation [31m(BETA Tool) [36mEvaluate gene expression from RNA-seq reads aligned to genome.[0m
[32m GetNormalArtifactData [36mCollects data for training normal artifact filter[0m
[32m GetPileupSummaries [36mTabulates pileup metrics for inferring contamination[0m
[32m LocalAssembler [31m(BETA Tool) [36mLocal assembler for SVs[0m
[32m Pileup [36mPrints read alignments in samtools pileup format[0m
[32m PileupSpark [31m(BETA Tool) [36mPrints read alignments in samtools pileup format[0m
[37m--------------------------------------------------------------------------------------
[0m[31mDiagnostics and Quality Control: Tools that collect sequencing quality related and comparative metrics[0m
[32m AccumulateQualityYieldMetrics (Picard) [36mCombines multiple QualityYieldMetrics files into a single file.[0m
[32m AccumulateVariantCallingMetrics (Picard) [36mCombines multiple Variant Calling Metrics files into a single file[0m
[32m AnalyzeCovariates [36mEvaluate and compare base quality score recalibration (BQSR) tables[0m
[32m BamIndexStats (Picard) [36mGenerate index statistics from a BAM file[0m
[32m CalcMetadataSpark [31m(BETA Tool) [36m(Internal) Collects read metrics relevant to structural variant discovery[0m
[32m CalculateContamination [36mCalculate the fraction of reads coming from cross-sample contamination[0m
[32m CalculateFingerprintMetrics (Picard) [36mCalculate statistics on fingerprints, checking their viability[0m
[32m CalculateReadGroupChecksum (Picard) [36mCreates a hash code based on the read groups (RG). [0m
[32m CheckDuplicateMarking (Picard) [36mChecks the consistency of duplicate markings.[0m
[32m CheckFingerprint (Picard) [36mComputes a fingerprint from the supplied input (SAM/BAM/CRAM or VCF) file and compares it to the provided genotypes[0m
[32m CheckPileup [36mCompare GATK's internal pileup to a reference Samtools mpileup[0m
[32m CheckTerminatorBlock (Picard) [36mAsserts the provided gzip file's (e.g., BAM) last block is well-formed; RC 100 otherwise[0m
[32m ClusterCrosscheckMetrics (Picard) [36mClusters the results of a CrosscheckFingerprints run by LOD score[0m
[32m CollectAlignmentSummaryMetrics (Picard) [36mProduces a summary of alignment metrics from a SAM or BAM file. [0m
[32m CollectArraysVariantCallingMetrics (Picard) [36mCollects summary and per-sample from the provided arrays VCF file[0m
[32m CollectBaseDistributionByCycle (Picard) [36mChart the nucleotide distribution per cycle in a SAM or BAM file[0m
[32m CollectBaseDistributionByCycleSpark [31m(BETA Tool) [36mCollects base distribution per cycle in SAM/BAM/CRAM file(s).[0m
[32m CollectGcBiasMetrics (Picard) [36mCollect metrics regarding GC bias. [0m
[32m CollectHiSeqXPfFailMetrics (Picard) [36mClassify PF-Failing reads in a HiSeqX Illumina Basecalling directory into various categories.[0m
[32m CollectHsMetrics (Picard) [36mCollects hybrid-selection (HS) metrics for a SAM or BAM file. [0m
[32m CollectIndependentReplicateMetrics (Picard) [31m(EXPERIMENTAL Tool) [36mEstimates the rate of independent replication rate of reads within a bam.
[0m
[32m CollectInsertSizeMetrics (Picard) [36mCollect metrics about the insert size distribution of a paired-end library. [0m
[32m CollectInsertSizeMetricsSpark [31m(BETA Tool) [36mCollects insert size distribution information on alignment data[0m
[32m CollectJumpingLibraryMetrics (Picard) [36mCollect jumping library metrics. [0m
[32m CollectMultipleMetrics (Picard) [36mCollect multiple classes of metrics. [0m
[32m CollectMultipleMetricsSpark [31m(BETA Tool) [36mRuns multiple metrics collection modules for a given alignment file[0m
[32m CollectOxoGMetrics (Picard) [36mCollect metrics to assess oxidative artifacts.[0m
[32m CollectQualityYieldMetrics (Picard) [36mCollect metrics about reads that pass quality thresholds and Illumina-specific filters. [0m
[32m CollectQualityYieldMetricsSpark [31m(BETA Tool) [36mCollects quality yield metrics from SAM/BAM/CRAM file(s).[0m
[32m CollectRawWgsMetrics (Picard) [36mCollect whole genome sequencing-related metrics. [0m
[32m CollectRnaSeqMetrics (Picard) [36mProduces RNA alignment metrics for a SAM or BAM file. [0m
[32m CollectRrbsMetrics (Picard) [36mCollects metrics from reduced representation bisulfite sequencing (Rrbs) data. [0m
[32m CollectSamErrorMetrics (Picard) [36mProgram to collect error metrics on bases stratified in various ways.[0m
[32m CollectSequencingArtifactMetrics (Picard) [36mCollect metrics to quantify single-base sequencing artifacts. [0m
[32m CollectTargetedPcrMetrics (Picard) [36mCalculate PCR-related metrics from targeted sequencing data. [0m
[32m CollectVariantCallingMetrics (Picard) [36mCollects per-sample and aggregate (spanning all samples) metrics from the provided VCF file[0m
[32m CollectWgsMetrics (Picard) [36mCollect metrics about coverage and performance of whole genome sequencing (WGS) experiments.[0m
[32m CollectWgsMetricsWithNonZeroCoverage (Picard)[31m(EXPERIMENTAL Tool) [36mCollect metrics about coverage and performance of whole genome sequencing (WGS) experiments. [0m
[32m CompareBaseQualities [36mCompares the base qualities of two SAM/BAM/CRAM files[0m
[32m CompareDuplicatesSpark [31m(BETA Tool) [36mDetermine if two potentially identical BAMs have the same duplicate reads[0m
[32m CompareMetrics (Picard) [36mCompare two metrics files.[0m
[32m CompareSAMs (Picard) [36mCompare two input SAM/BAM/CRAM files. [0m
[32m ConvertHaplotypeDatabaseToVcf (Picard) [36mConvert Haplotype database file to vcf[0m
[32m ConvertSequencingArtifactToOxoG (Picard) [36mExtract OxoG metrics from generalized artifacts metrics. [0m
[32m CrosscheckFingerprints (Picard) [36mChecks that all data in the input files appear to have come from the same individual[0m
[32m CrosscheckReadGroupFingerprints (Picard) [36mDEPRECATED: USE CrosscheckFingerprints. [0m
[32m DumpTabixIndex [36mDumps a tabix index file.[0m
[32m EstimateLibraryComplexity (Picard) [36mEstimates the numbers of unique molecules in a sequencing library. [0m
[32m ExtractFingerprint (Picard) [36mComputes a fingerprint from the input file.[0m
[32m FlagStat [36mAccumulate flag statistics given a BAM file[0m
[32m FlagStatSpark [36mSpark tool to accumulate flag statistics[0m
[32m GatherPileupSummaries [36mCombine output files from GetPileupSummary in the order defined by a sequence dictionary[0m
[32m GetSampleName [36mEmit a single sample name[0m
[32m IdentifyContaminant (Picard) [36mComputes a fingerprint from the supplied SAM/BAM file, given a contamination estimate.[0m
[32m LiftOverHaplotypeMap (Picard) [36mLifts over a haplotype database from one reference to another[0m
[32m MeanQualityByCycle (Picard) [36mCollect mean quality by cycle.[0m
[32m MeanQualityByCycleSpark [31m(BETA Tool) [36mMeanQualityByCycle on Spark[0m
[32m QualityScoreDistribution (Picard) [36mChart the distribution of quality scores. [0m
[32m QualityScoreDistributionSpark [31m(BETA Tool) [36mQualityScoreDistribution on Spark[0m
[32m ValidateSamFile (Picard) [36mValidates a SAM/BAM/CRAM file.[0m
[32m ViewSam (Picard) [36mPrints a SAM or BAM file to the screen[0m
[37m--------------------------------------------------------------------------------------
[0m[31mExample Tools: Example tools that show developers how to implement new tools[0m
[32m ExampleMultiFeatureWalker [36mExample of a MultiFeatureWalker subclass.[0m
[32m HtsgetReader [31m(EXPERIMENTAL Tool) [36mDownload a file using htsget[0m
[37m--------------------------------------------------------------------------------------
[0m[31mFlow Based Tools: Tools designed specifically to operate on flow based data[0m
[32m CalculateAverageCombinedAnnotations [31m(EXPERIMENTAL Tool) [36mDivides annotations that were summed by genomicsDB by number of samples to calculate average.[0m
[32m FlowFeatureMapper [31m(EXPERIMENTAL Tool) [36mMap/find features in BAM file, output VCF. Initially mapping SNVs[0m
[32m GroundTruthReadsBuilder [31m(EXPERIMENTAL Tool) [36mProduces a flexible and robust ground truth set for base calling training[0m
[32m SplitCRAM [31m(EXPERIMENTAL Tool) [36mSplit CRAM files to smaller files efficiently[0m
[37m--------------------------------------------------------------------------------------
[0m[31mGenotyping Arrays Manipulation: Tools that manipulate data generated by Genotyping arrays[0m
[32m BpmToNormalizationManifestCsv (Picard) [36mProgram to convert an Illumina bpm file into a bpm.csv file.[0m
[32m CombineGenotypingArrayVcfs (Picard) [36mProgram to combine multiple genotyping array VCF files into one VCF.[0m
[32m CompareGtcFiles (Picard) [36mCompares two GTC files.[0m
[32m CreateBafRegressMetricsFile (Picard) [36mProgram to generate a picard metrics file from the output of the bafRegress tool.[0m
[32m CreateExtendedIlluminaManifest (Picard) [36mCreate an Extended Illumina Manifest for usage by the Picard tool GtcToVcf[0m
[32m CreateVerifyIDIntensityContaminationMetricsFile (Picard) [36mProgram to generate a picard metrics file from the output of the VerifyIDIntensity tool.[0m
[32m GtcToVcf (Picard) [36mProgram to convert an Illumina GTC file to a VCF[0m
[32m MergePedIntoVcf (Picard) [36mProgram to merge a single-sample ped file from zCall into a single-sample VCF.[0m
[32m VcfToAdpc (Picard) [36mProgram to convert an Arrays VCF to an ADPC file.[0m
[37m--------------------------------------------------------------------------------------
[0m[31mIntervals Manipulation: Tools that process genomic intervals in various formats[0m
[32m BedToIntervalList (Picard) [36mConverts a BED file to a Picard Interval List. [0m
[32m CompareIntervalLists [36mCompare two interval lists for equality[0m
[32m IntervalListToBed (Picard) [36mConverts an Picard IntervalList file to a BED file.[0m
[32m IntervalListTools (Picard) [36mA tool for performing various IntervalList manipulations[0m
[32m LiftOverIntervalList (Picard) [36mLifts over an interval list from one reference build to another. [0m
[32m PreprocessIntervals [36mPrepares bins for coverage collection[0m
[32m SplitIntervals [36mSplit intervals into sub-interval files.[0m
[37m--------------------------------------------------------------------------------------
[0m[31mMetagenomics: Tools that perform metagenomic analysis, e.g. microbial community composition and pathogen detection[0m
[32m PathSeqBuildKmers [36mBuilds set of host reference k-mers[0m
[32m PathSeqBuildReferenceTaxonomy [36mBuilds a taxonomy datafile of the microbe reference[0m
[32m PathSeqBwaSpark [36mStep 2: Aligns reads to the microbe reference[0m
[32m PathSeqFilterSpark [36mStep 1: Filters low quality, low complexity, duplicate, and host reads[0m
[32m PathSeqPipelineSpark [36mCombined tool that performs all steps: read filtering, microbe reference alignment, and abundance scoring[0m
[32m PathSeqScoreSpark [36mStep 3: Classifies pathogen-aligned reads and generates abundance scores[0m
[37m--------------------------------------------------------------------------------------
[0m[31mMethylation-Specific Tools: Tools that perform methylation calling, processing bisulfite sequenced, methylation-aware aligned BAM[0m
[32m MethylationTypeCaller [31m(EXPERIMENTAL Tool) [36mIdentify methylated bases from bisulfite sequenced, methylation-aware BAMs[0m
[37m--------------------------------------------------------------------------------------
[0m[31mOther: Miscellaneous tools, e.g. those that aid in data streaming[0m
[32m CreateHadoopBamSplittingIndex [31m(BETA Tool) [36mCreate a Hadoop BAM splitting index[0m
[32m FifoBuffer (Picard) [36mProvides a large, FIFO buffer that can be used to buffer input and output streams between programs.[0m
[32m GatherBQSRReports [36mGathers scattered BQSR recalibration reports into a single file[0m
[32m GatherTranches [31m(BETA Tool) [36mGathers scattered VQSLOD tranches into a single file[0m
[32m IndexFeatureFile [36mCreates an index for a feature file, e.g. VCF or BED file.[0m
[32m ParallelCopyGCSDirectoryIntoHDFSSpark [31m(BETA Tool) [36mParallel copy a file or directory from Google Cloud Storage into the HDFS file system used by Spark[0m
[32m PrintBGZFBlockInformation [31m(EXPERIMENTAL Tool) [36mPrint information about the compressed blocks in a BGZF format file[0m
[32m ReadAnonymizer [31m(EXPERIMENTAL Tool) [36mReplace bases in reads with reference bases.[0m
[32m ReblockGVCF [36mCondenses homRef blocks in a single-sample GVCF[0m
[32m SortGff (Picard) [36mSorts a gff3 file, and adds flush directives[0m
[37m--------------------------------------------------------------------------------------
[0m[31mRead Data Manipulation: Tools that manipulate read data in SAM, BAM or CRAM format[0m
[32m AddCommentsToBam (Picard) [36mAdds comments to the header of a BAM file.[0m
[32m AddOATag (Picard) [36mRecord current alignment information to OA tag.[0m
[32m AddOrReplaceReadGroups (Picard) [36mAssigns all the reads in a file to a single new read-group.[0m
[32m AddOriginalAlignmentTags [31m(EXPERIMENTAL Tool) [36mAdds Original Alignment tag and original mate contig tag[0m
[32m ApplyBQSR [36mApply base quality score recalibration[0m
[32m ApplyBQSRSpark [31m(BETA Tool) [36mApply base quality score recalibration on Spark[0m
[32m BQSRPipelineSpark [31m(BETA Tool) [36mBoth steps of BQSR (BaseRecalibrator and ApplyBQSR) on Spark[0m
[32m BamToBfq (Picard) [36mConverts a BAM file into a BFQ (binary fastq formatted) file[0m
[32m BaseRecalibrator [36mGenerates recalibration table for Base Quality Score Recalibration (BQSR)[0m
[32m BaseRecalibratorSpark [31m(BETA Tool) [36mGenerate recalibration table for Base Quality Score Recalibration (BQSR) on Spark[0m
[32m BuildBamIndex (Picard) [36mGenerates a BAM index ".bai" file. [0m
[32m BwaAndMarkDuplicatesPipelineSpark [31m(BETA Tool) [36mTakes name-sorted file and runs BWA and MarkDuplicates.[0m
[32m BwaSpark [31m(BETA Tool) [36mAlign reads to a given reference using BWA on Spark[0m
[32m CleanSam (Picard) [36mCleans a SAM/BAM/CRAM files, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads[0m
[32m ClipReads [36mClip reads in a SAM/BAM/CRAM file[0m
[32m CollectDuplicateMetrics (Picard) [36mCollect Duplicate metrics from marked file.[0m
[32m ConvertHeaderlessHadoopBamShardToBam [31m(BETA Tool) [36mConvert a headerless BAM shard into a readable BAM[0m
[32m DownsampleByDuplicateSet [31m(BETA Tool) [36mDiscard a set fraction of duplicate sets from a UMI-grouped bam[0m
[32m DownsampleSam (Picard) [36mDownsample a SAM or BAM file.[0m
[32m ExtractOriginalAlignmentRecordsByNameSpark [31m(BETA Tool) [36mSubsets reads by name[0m
[32m FastqToSam (Picard) [36mConverts a FASTQ file to an unaligned BAM or SAM file[0m
[32m FilterSamReads (Picard) [36mSubsets reads from a SAM/BAM/CRAM file by applying one of several filters.[0m
[32m FixMateInformation (Picard) [36mVerify mate-pair information between mates and fix if needed.[0m
[32m FixMisencodedBaseQualityReads [36mFix Illumina base quality scores in a SAM/BAM/CRAM file[0m
[32m GatherBamFiles (Picard) [36mConcatenate efficiently BAM files that resulted from a scattered parallel analysis[0m
[32m LeftAlignIndels [36mLeft-aligns indels from reads in a SAM/BAM/CRAM file[0m
[32m MarkDuplicates (Picard) [36mIdentifies duplicate reads. [0m
[32m MarkDuplicatesSpark [36mMarkDuplicates on Spark[0m
[32m MarkDuplicatesWithMateCigar (Picard) [36mIdentifies duplicate reads, accounting for mate CIGAR. [0m
[32m MergeBamAlignment (Picard) [36mMerge alignment data from a SAM or BAM with data in an unmapped BAM file. [0m
[32m MergeSamFiles (Picard) [36mMerges multiple SAM/BAM/CRAM (and/or) files into a single file. [0m
[32m PositionBasedDownsampleSam (Picard) [36mDownsample a SAM or BAM file to retain a subset of the reads based on the reads location in each tile in the flowcell.[0m
[32m PostProcessReadsForRSEM [31m(BETA Tool) [36mReorder reads before running RSEM[0m
[32m PrintDistantMates [36mUnmaps reads with distant mates.[0m
[32m PrintReads [36mPrint reads in the SAM/BAM/CRAM file[0m
[32m PrintReadsHeader [36mPrint the header from a SAM/BAM/CRAM file[0m
[32m PrintReadsSpark [36mPrintReads on Spark[0m
[32m ReorderSam (Picard) [36mReorders reads in a SAM or BAM file to match ordering in a second reference file.[0m
[32m ReplaceSamHeader (Picard) [36mReplaces the SAMFileHeader in a SAM/BAM/CRAM file. [0m
[32m RevertBaseQualityScores [36mRevert Quality Scores in a SAM/BAM/CRAM file[0m
[32m RevertOriginalBaseQualitiesAndAddMateCigar (Picard)[36mReverts the original base qualities and adds the mate cigar tag to read-group files[0m
[32m RevertSam (Picard) [36mReverts SAM/BAM/CRAM files to a previous state. [0m
[32m RevertSamSpark [31m(BETA Tool) [36mReverts SAM, BAM or CRAM files to a previous state.[0m
[32m SamFormatConverter (Picard) [36mConvert a BAM file to a SAM file, or a SAM to a BAM[0m
[32m SamToFastq (Picard) [36mConverts a SAM/BAM/CRAM file to FASTQ.[0m
[32m SamToFastqWithTags (Picard) [36mConverts a SAM or BAM file to FASTQ alongside FASTQs created from tags.[0m
[32m SetNmAndUqTags (Picard) [36mDEPRECATED: Use SetNmMdAndUqTags instead.[0m
[32m SetNmMdAndUqTags (Picard) [36mFixes the NM, MD, and UQ tags in a SAM/BAM/CRAM file [0m
[32m SimpleMarkDuplicatesWithMateCigar (Picard) [31m(EXPERIMENTAL Tool) [36mExamines aligned records in the supplied SAM or BAM file to locate duplicate molecules.[0m
[32m SortSam (Picard) [36mSorts a SAM, BAM or CRAM file. [0m
[32m SortSamSpark [31m(BETA Tool) [36mSortSam on Spark (works on SAM/BAM/CRAM)[0m
[32m SplitNCigarReads [36mSplit Reads with N in Cigar[0m
[32m SplitReads [36mOutputs reads from a SAM/BAM/CRAM by read group, sample and library name[0m
[32m SplitSamByLibrary (Picard) [36mSplits a SAM/BAM/CRAM file into individual files by library[0m
[32m SplitSamByNumberOfReads (Picard) [36mSplits a SAM/BAM/CRAM file to multiple files.[0m
[32m TransferReadTags [31m(EXPERIMENTAL Tool) [36mIncorporate read tags in a SAM file to that of a matching SAM file[0m
[32m UmiAwareMarkDuplicatesWithMateCigar (Picard) [31m(EXPERIMENTAL Tool) [36mIdentifies duplicate reads using information from read positions and UMIs. [0m
[32m UnmarkDuplicates [36mClears the 0x400 duplicate SAM flag[0m
[37m--------------------------------------------------------------------------------------
[0m[31mReference: Tools that analyze and manipulate FASTA format references[0m
[32m BaitDesigner (Picard) [36mDesigns oligonucleotide baits for hybrid selection reactions.[0m
[32m BwaMemIndexImageCreator [36mCreate a BWA-MEM index image file for use with GATK BWA tools[0m
[32m CheckReferenceCompatibility [31m(EXPERIMENTAL Tool) [36mCheck a BAM/VCF for compatibility against specified references.[0m
[32m CompareReferences [31m(EXPERIMENTAL Tool) [36mDisplay reference comparison as a tab-delimited table and summarize reference differences.[0m
[32m ComposeSTRTableFile [36mComposes a genome-wide STR location table used for DragSTR model auto-calibration[0m
[32m CountBasesInReference [36mCount the numbers of each base in a reference file[0m
[32m CreateSequenceDictionary (Picard) [36mCreates a sequence dictionary for a reference sequence. [0m
[32m ExtractSequences (Picard) [36mSubsets intervals from a reference sequence to a new FASTA file.[0m
[32m FastaAlternateReferenceMaker [36mCreate an alternative reference by combining a fasta with a vcf.[0m
[32m FastaReferenceMaker [36mCreate snippets of a fasta file[0m
[32m FindBadGenomicKmersSpark [31m(BETA Tool) [36mIdentifies sequences that occur at high frequency in a reference[0m
[32m NonNFastaSize (Picard) [36mCounts the number of non-N bases in a fasta file.[0m
[32m NormalizeFasta (Picard) [36mNormalizes lines of sequence in a FASTA file to be of the same length.[0m
[32m ScatterIntervalsByNs (Picard) [36mWrites an interval list created by splitting a reference at Ns.[0m
[32m ShiftFasta [31m(BETA Tool) [36mCreates a shifted fasta file and shift_back file[0m
[37m--------------------------------------------------------------------------------------
[0m[31mShort Variant Discovery: Tools that perform variant calling and genotyping for short variants (SNPs, SNVs and Indels)[0m
[32m CalibrateDragstrModel [36mestimates the parameters for the DRAGstr model[0m
[32m CombineGVCFs [36mMerges one or more HaplotypeCaller GVCF files into a single GVCF with appropriate annotations[0m
[32m GenomicsDBImport [36mImport VCFs to GenomicsDB[0m
[32m GenotypeGVCFs [36mPerform joint genotyping on one or more samples pre-called with HaplotypeCaller[0m
[32m GnarlyGenotyper [31m(BETA Tool) [36mPerform "quick and dirty" joint genotyping on one or more samples pre-called with HaplotypeCaller[0m
[32m HaplotypeBasedVariantRecaller [31m(EXPERIMENTAL Tool) [36mCalculate likelihood matrix for each Allele in VCF against a set of Reads limited by a set of Haplotypes[0m
[32m HaplotypeCaller [36mCall germline SNPs and indels via local re-assembly of haplotypes[0m
[32m HaplotypeCallerSpark [31m(BETA Tool) [36mHaplotypeCaller on Spark[0m
[32m LearnReadOrientationModel [36mGet the maximum likelihood estimates of artifact prior probabilities in the orientation bias mixture model filter[0m
[32m MergeMutectStats [36mMerge the stats output by scatters of a single Mutect2 job[0m
[32m Mutect2 [36mCall somatic SNVs and indels via local assembly of haplotypes[0m
[32m RampedHaplotypeCaller [31m(EXPERIMENTAL Tool) [36mCall germline SNPs and indels via local re-assembly of haplotypes (ramped version)[0m
[32m ReadsPipelineSpark [31m(BETA Tool) [36mRuns BWA (if specified), MarkDuplicates, BQSR, and HaplotypeCaller on unaligned or aligned reads to generate a VCF.[0m
[37m--------------------------------------------------------------------------------------
[0m[31mStructural Variant Discovery: Tools that detect structural variants [0m
[32m CollectSVEvidence [31m(BETA Tool) [36mGathers paired-end and split read evidence files for use in the GATK-SV pipeline.[0m
[32m CondenseDepthEvidence [31m(EXPERIMENTAL Tool) [36mMerges adjacent DepthEvidence records.[0m
[32m CpxVariantReInterpreterSpark [31m(BETA Tool) [36m(Internal) Tries to extract simple variants from a provided GATK-SV CPX.vcf[0m
[32m DiscoverVariantsFromContigAlignmentsSAMSpark [31m(BETA Tool) [36m(Internal) Examines aligned contigs from local assemblies and calls structural variants[0m
[32m ExtractSVEvidenceSpark [31m(BETA Tool) [36m(Internal) Extracts evidence of structural variations from reads[0m
[32m FindBreakpointEvidenceSpark [31m(BETA Tool) [36m(Internal) Produces local assemblies of genomic regions that may harbor structural variants[0m
[32m JointGermlineCNVSegmentation [31m(BETA Tool) [36mCombine segmented gCNV VCFs.[0m
[32m PrintReadCounts [31m(EXPERIMENTAL Tool) [36mPrints count files for CNV determination.[0m
[32m PrintSVEvidence [31m(EXPERIMENTAL Tool) [36mMerges SV evidence records.[0m
[32m SVAnnotate [36mAdds gene overlap and variant consequence annotations to SV VCF from GATK-SV pipeline[0m
[32m SVCluster [31m(BETA Tool) [36mClusters structural variants[0m
[32m SiteDepthtoBAF [31m(EXPERIMENTAL Tool) [36mConvert SiteDepth to BafEvidence[0m
[32m StructuralVariantDiscoverer [31m(BETA Tool) [36m(Internal) Examines aligned contigs from local assemblies and calls structural variants or their breakpoints[0m
[32m StructuralVariationDiscoveryPipelineSpark [31m(BETA Tool) [36mRuns the structural variation discovery workflow on a single sample[0m
[32m SvDiscoverFromLocalAssemblyContigAlignmentsSpark [31m(BETA Tool) [36m(Internal) Examines aligned contigs from local assemblies and calls structural variants or their breakpoints[0m
[37m--------------------------------------------------------------------------------------
[0m[31mVariant Evaluation and Refinement: Tools that evaluate and refine variant calls, e.g. with annotations not offered by the engine[0m
[32m AlleleFrequencyQC [31m(BETA Tool) [36mGeneral-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more)[0m
[32m AnnotateVcfWithBamDepth [36m(Internal) Annotate a vcf with a bam's read depth at each variant locus[0m
[32m AnnotateVcfWithExpectedAlleleFraction [36m(Internal) Annotate a vcf with expected allele fractions in pooled sequencing[0m
[32m CalculateGenotypePosteriors [36mCalculate genotype posterior probabilities given family and/or known population genotypes[0m
[32m CalculateMixingFractions [36m(Internal) Calculate proportions of different samples in a pooled bam[0m
[32m Concordance [36mEvaluate concordance of an input VCF against a validated truth VCF[0m
[32m CountFalsePositives [31m(BETA Tool) [36mCount PASS variants[0m
[32m CountVariants [36mCounts variant records in a VCF file, regardless of filter status.[0m
[32m CountVariantsSpark [36mCountVariants on Spark[0m
[32m EvaluateInfoFieldConcordance [31m(BETA Tool) [36mEvaluate concordance of info fields in an input VCF against a validated truth VCF[0m
[32m FilterFuncotations [31m(EXPERIMENTAL Tool) [36mFilter variants based on clinically-significant Funcotations.[0m
[32m FindMendelianViolations (Picard) [36mFinds mendelian violations of all types within a VCF[0m
[32m FuncotateSegments [31m(BETA Tool) [36mFunctional annotation for segment files. The output formats are not well-defined and subject to change.[0m
[32m Funcotator [36mFunctional Annotator[0m
[32m FuncotatorDataSourceDownloader [36mData source downloader for Funcotator.[0m
[32m GenotypeConcordance (Picard) [36mCalculates the concordance between genotype data of one sample in each of two VCFs - truth (or reference) vs. calls.[0m
[32m MergeMutect2CallsWithMC3 [31m(EXPERIMENTAL Tool) [36mUNSUPPORTED. FOR EVALUATION ONLY. Merge M2 calls with MC[0m
[32m ReferenceBlockConcordance [36mEvaluate GVCF reference block concordance of an input GVCF against a truth GVCF[0m
[32m ValidateBasicSomaticShortMutations [31m(EXPERIMENTAL Tool) [36mCheck variants against tumor-normal bams representing the same samples, though not the ones from the actual calls.[0m
[32m ValidateVariants [36mValidate VCF[0m
[32m VariantEval [31m(BETA Tool) [36mGeneral-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more)[0m
[32m VariantsToTable [36mExtract fields from a VCF file to a tab-delimited table[0m
[37m--------------------------------------------------------------------------------------
[0m[31mVariant Filtering: Tools that filter variants by annotating the FILTER column[0m
[32m ApplyVQSR [36m Apply a score cutoff to filter variants based on a recalibration table[0m
[32m CNNScoreVariants [36mApply a Convolutional Neural Net to filter annotated variants[0m
[32m CNNVariantTrain [31m(EXPERIMENTAL Tool) [36mTrain a CNN model for filtering variants[0m
[32m CNNVariantWriteTensors [31m(EXPERIMENTAL Tool) [36mWrite variant tensors for training a CNN to filter variants[0m
[32m CreateSomaticPanelOfNormals [31m(BETA Tool) [36mMake a panel of normals for use with Mutect2[0m
[32m ExtractVariantAnnotations [31m(BETA Tool) [36mExtracts site-level variant annotations, labels, and other metadata from a VCF file to HDF5 files[0m
[32m FilterAlignmentArtifacts [31m(EXPERIMENTAL Tool) [36mFilter alignment artifacts from a vcf callset.[0m
[32m FilterMutectCalls [36mFilter somatic SNVs and indels called by Mutect2[0m
[32m FilterVariantTranches [36mApply tranche filtering[0m
[32m FilterVcf (Picard) [36mHard filters a VCF.[0m
[32m MTLowHeteroplasmyFilterTool [36mIf too many low het sites, filter all low het sites[0m
[32m NuMTFilterTool [36mUses the median autosomal coverage and the allele depth to determine whether the allele might be a NuMT[0m
[32m ScoreVariantAnnotations [31m(BETA Tool) [36mScores variant calls in a VCF file based on site-level annotations using a previously trained model[0m
[32m TrainVariantAnnotationsModel [31m(BETA Tool) [36mTrains a model for scoring variant calls based on site-level annotations[0m
[32m VariantFiltration [36mFilter variant calls based on INFO and/or FORMAT annotations[0m
[32m VariantRecalibrator [36mBuild a recalibration model to score variant quality for filtering purposes[0m
[37m--------------------------------------------------------------------------------------
[0m[31mVariant Manipulation: Tools that manipulate variant call format (VCF) data[0m
[32m FixVcfHeader (Picard) [36mReplaces or fixes a VCF header.[0m
[32m GatherVcfs (Picard) [36mGathers multiple VCF files from a scatter operation into a single VCF file[0m
[32m GatherVcfsCloud [31m(BETA Tool) [36mGathers multiple VCF files from a scatter operation into a single VCF file[0m
[32m LeftAlignAndTrimVariants [36mLeft align and trim vairants[0m
[32m LiftoverVcf (Picard) [36mLifts over a VCF file from one reference build to another. [0m
[32m MakeSitesOnlyVcf (Picard) [36mCreates a VCF that contains all the site-level information for all records in the input VCF but no genotype information.[0m
[32m MakeVcfSampleNameMap (Picard) [36mCreates a TSV from sample name to VCF/GVCF path, with one line per input.[0m
[32m MergeVcfs (Picard) [36mCombines multiple variant files into a single variant file[0m
[32m PrintVariantsSpark [36mPrints out variants from the input VCF.[0m
[32m RemoveNearbyIndels [36m(Internal) Remove indels from the VCF file that are close to each other.[0m
[32m RenameSampleInVcf (Picard) [36mRenames a sample within a VCF or BCF.[0m
[32m SelectVariants [36mSelect a subset of variants from a VCF file[0m
[32m SortVcf (Picard) [36mSorts one or more VCF files. [0m
[32m SplitVcfs (Picard) [36mSplits SNPs and INDELs into separate files. [0m
[32m UpdateVCFSequenceDictionary [36mUpdates the sequence dictionary in a variant file.[0m
[32m UpdateVcfSequenceDictionary (Picard) [36mTakes a VCF and a second file that contains a sequence dictionary and updates the VCF with the new sequence dictionary.[0m
[32m VariantAnnotator [36mTool for adding annotations to VCF files[0m
[32m VcfFormatConverter (Picard) [36mConverts VCF to BCF or BCF to VCF. [0m
[32m VcfToIntervalList (Picard) [36mConverts a VCF or BCF file to a Picard Interval List[0m
[37m--------------------------------------------------------------------------------------
[0m
***********************************************************************
A USER ERROR has occurred: '-Xmx104857M' is not a valid command.
***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
Using GATK jar /gatk/gatk-package-4.3.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /gatk/gatk-package-4.3.0.0-local.jar -Xmx104857M SplitNCigarReads -R input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta -I output.temp/Le1-1-501-701_1.fastq.gz_addrg_repN.bam -O output2/Le1-1-501-701_1.fastq.gz.bam
/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
INFO 2023-02-28 23:40:33 AddOrReplaceReadGroups
********** NOTE: Picard's command line syntax is changing.
**********
********** For more information, please see:
********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
**********
********** The command line looks like this in the new syntax:
**********
********** AddOrReplaceReadGroups -I output/Le1-12-501-708_1.fastq.gz.bam -O output.temp/Le1-12-501-708_1.fastq.gz_addrg.bam -SO coordinate -RGID Le1-12-501-708_1.fastq.gz -RGLB library -RGPL Illumina -RGPU Illumina -RGSM Le1-12-501-708_1.fastq.gz
**********
23:40:34.049 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/picard-2.18.27-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Tue Feb 28 23:40:34 GMT 2023] AddOrReplaceReadGroups INPUT=output/Le1-12-501-708_1.fastq.gz.bam OUTPUT=output.temp/Le1-12-501-708_1.fastq.gz_addrg.bam SORT_ORDER=coordinate RGID=Le1-12-501-708_1.fastq.gz RGLB=library RGPL=Illumina RGPU=Illumina RGSM=Le1-12-501-708_1.fastq.gz VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Tue Feb 28 23:40:34 GMT 2023] Executing as ?@04a734825eac on Linux 3.10.0-1160.36.2.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.27-SNAPSHOT
INFO 2023-02-28 23:40:34 AddOrReplaceReadGroups Created read-group ID=Le1-12-501-708_1.fastq.gz PL=Illumina LB=library SM=Le1-12-501-708_1.fastq.gz
[Tue Feb 28 23:40:34 GMT 2023] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2147483648
[1m[31mUSAGE: [32m[1m[31m [-h]
[0m[1m[31mAvailable Programs:
[0m[37m--------------------------------------------------------------------------------------
[0m[31mBase Calling: Tools that process sequencing machine data, e.g. Illumina base calls, and detect sequencing level attributes, e.g. adapters[0m
[32m CheckIlluminaDirectory (Picard) [36mAsserts the validity for specified Illumina basecalling data. [0m
[32m CollectIlluminaBasecallingMetrics (Picard) [36mCollects Illumina Basecalling metrics for a sequencing run. [0m
[32m CollectIlluminaLaneMetrics (Picard) [36mCollects Illumina lane metrics for the given BaseCalling analysis directory.[0m
[32m ExtractIlluminaBarcodes (Picard) [36mTool determines the barcode for each read in an Illumina lane. [0m
[32m IlluminaBasecallsToFastq (Picard) [36mGenerate FASTQ file(s) from Illumina basecall read data. [0m
[32m IlluminaBasecallsToSam (Picard) [36mTransforms raw Illumina sequencing data into an unmapped SAM, BAM or CRAM file.[0m
[32m MarkIlluminaAdapters (Picard) [36mReads a SAM/BAM/CRAM file and rewrites it with new adapter-trimming tags. [0m
[37m--------------------------------------------------------------------------------------
[0m[31mCopy Number Variant Discovery: Tools that analyze read coverage to detect copy number variants.[0m
[32m AnnotateIntervals [36mAnnotates intervals with GC content, mappability, and segmental-duplication content[0m
[32m CallCopyRatioSegments [36mCalls copy-ratio segments as amplified, deleted, or copy-number neutral[0m
[32m CombineSegmentBreakpoints [31m(EXPERIMENTAL Tool) [36mCombine the breakpoints of two segment files and annotate the resulting intervals with chosen columns from each file.[0m
[32m CreateReadCountPanelOfNormals [36mCreates a panel of normals for read-count denoising[0m
[32m DenoiseReadCounts [36mDenoises read counts to produce denoised copy ratios[0m
[32m DetermineGermlineContigPloidy [36mDetermines the baseline contig ploidy for germline samples given counts data[0m
[32m FilterIntervals [36mFilters intervals based on annotations and/or count statistics[0m
[32m GermlineCNVCaller [36mCalls copy-number variants in germline samples given their counts and the output of DetermineGermlineContigPloidy[0m
[32m MergeAnnotatedRegions [31m(EXPERIMENTAL Tool) [36mMerge annotated genomic regions based entirely on touching/overlapping intervals.[0m
[32m MergeAnnotatedRegionsByAnnotation [31m(EXPERIMENTAL Tool) [36mMerge annotated genomic regions within specified distance if annotation value(s) are exactly the same.[0m
[32m ModelSegments [36mModels segmented copy ratios from denoised copy ratios and segmented minor-allele fractions from allelic counts[0m
[32m PlotDenoisedCopyRatios [36mCreates plots of denoised copy ratios[0m
[32m PlotModeledSegments [36mCreates plots of denoised and segmented copy-ratio and minor-allele-fraction estimates[0m
[32m PostprocessGermlineCNVCalls [36mPostprocesses the output of GermlineCNVCaller and generates VCFs and denoised copy ratios[0m
[32m TagGermlineEvents [31m(EXPERIMENTAL Tool) [36mDo a simplistic tagging of germline events in a tumor segment file.[0m
[37m--------------------------------------------------------------------------------------
[0m[31mCoverage Analysis: Tools that count coverage, e.g. depth per allele[0m
[32m ASEReadCounter [36mGenerates table of filtered base counts at het sites for allele specific expression[0m
[32m AnalyzeSaturationMutagenesis [31m(BETA Tool) [36m(EXPERIMENTAL) Processes reads from a MITESeq or other saturation mutagenesis experiment.[0m
[32m CollectAllelicCounts [36mCollects reference and alternate allele counts at specified sites[0m
[32m CollectAllelicCountsSpark [36mCollects reference and alternate allele counts at specified sites[0m
[32m CollectF1R2Counts [36mCollect F1R2 read counts for the Mutect2 orientation bias mixture model filter[0m
[32m CollectReadCounts [36mCollects read counts at specified intervals[0m
[32m CountBases [36mCount bases in a SAM/BAM/CRAM file[0m
[32m CountBasesSpark [36mCounts bases in the input SAM/BAM[0m
[32m CountReads [36mCount reads in a SAM/BAM/CRAM file[0m
[32m CountReadsSpark [36mCounts reads in the input SAM/BAM[0m
[32m DepthOfCoverage [31m(BETA Tool) [36mGenerate coverage summary information for reads data[0m
[32m GatherNormalArtifactData [36mCombine output files from GetNormalArtifactData in the order defined by a sequence dictionary[0m
[32m GeneExpressionEvaluation [31m(BETA Tool) [36mEvaluate gene expression from RNA-seq reads aligned to genome.[0m
[32m GetNormalArtifactData [36mCollects data for training normal artifact filter[0m
[32m GetPileupSummaries [36mTabulates pileup metrics for inferring contamination[0m
[32m LocalAssembler [31m(BETA Tool) [36mLocal assembler for SVs[0m
[32m Pileup [36mPrints read alignments in samtools pileup format[0m
[32m PileupSpark [31m(BETA Tool) [36mPrints read alignments in samtools pileup format[0m
[37m--------------------------------------------------------------------------------------
[0m[31mDiagnostics and Quality Control: Tools that collect sequencing quality related and comparative metrics[0m
[32m AccumulateQualityYieldMetrics (Picard) [36mCombines multiple QualityYieldMetrics files into a single file.[0m
[32m AccumulateVariantCallingMetrics (Picard) [36mCombines multiple Variant Calling Metrics files into a single file[0m
[32m AnalyzeCovariates [36mEvaluate and compare base quality score recalibration (BQSR) tables[0m
[32m BamIndexStats (Picard) [36mGenerate index statistics from a BAM file[0m
[32m CalcMetadataSpark [31m(BETA Tool) [36m(Internal) Collects read metrics relevant to structural variant discovery[0m
[32m CalculateContamination [36mCalculate the fraction of reads coming from cross-sample contamination[0m
[32m CalculateFingerprintMetrics (Picard) [36mCalculate statistics on fingerprints, checking their viability[0m
[32m CalculateReadGroupChecksum (Picard) [36mCreates a hash code based on the read groups (RG). [0m
[32m CheckDuplicateMarking (Picard) [36mChecks the consistency of duplicate markings.[0m
[32m CheckFingerprint (Picard) [36mComputes a fingerprint from the supplied input (SAM/BAM/CRAM or VCF) file and compares it to the provided genotypes[0m
[32m CheckPileup [36mCompare GATK's internal pileup to a reference Samtools mpileup[0m
[32m CheckTerminatorBlock (Picard) [36mAsserts the provided gzip file's (e.g., BAM) last block is well-formed; RC 100 otherwise[0m
[32m ClusterCrosscheckMetrics (Picard) [36mClusters the results of a CrosscheckFingerprints run by LOD score[0m
[32m CollectAlignmentSummaryMetrics (Picard) [36mProduces a summary of alignment metrics from a SAM or BAM file. [0m
[32m CollectArraysVariantCallingMetrics (Picard) [36mCollects summary and per-sample from the provided arrays VCF file[0m
[32m CollectBaseDistributionByCycle (Picard) [36mChart the nucleotide distribution per cycle in a SAM or BAM file[0m
[32m CollectBaseDistributionByCycleSpark [31m(BETA Tool) [36mCollects base distribution per cycle in SAM/BAM/CRAM file(s).[0m
[32m CollectGcBiasMetrics (Picard) [36mCollect metrics regarding GC bias. [0m
[32m CollectHiSeqXPfFailMetrics (Picard) [36mClassify PF-Failing reads in a HiSeqX Illumina Basecalling directory into various categories.[0m
[32m CollectHsMetrics (Picard) [36mCollects hybrid-selection (HS) metrics for a SAM or BAM file. [0m
[32m CollectIndependentReplicateMetrics (Picard) [31m(EXPERIMENTAL Tool) [36mEstimates the rate of independent replication rate of reads within a bam.
[0m
[32m CollectInsertSizeMetrics (Picard) [36mCollect metrics about the insert size distribution of a paired-end library. [0m
[32m CollectInsertSizeMetricsSpark [31m(BETA Tool) [36mCollects insert size distribution information on alignment data[0m
[32m CollectJumpingLibraryMetrics (Picard) [36mCollect jumping library metrics. [0m
[32m CollectMultipleMetrics (Picard) [36mCollect multiple classes of metrics. [0m
[32m CollectMultipleMetricsSpark [31m(BETA Tool) [36mRuns multiple metrics collection modules for a given alignment file[0m
[32m CollectOxoGMetrics (Picard) [36mCollect metrics to assess oxidative artifacts.[0m
[32m CollectQualityYieldMetrics (Picard) [36mCollect metrics about reads that pass quality thresholds and Illumina-specific filters. [0m
[32m CollectQualityYieldMetricsSpark [31m(BETA Tool) [36mCollects quality yield metrics from SAM/BAM/CRAM file(s).[0m
[32m CollectRawWgsMetrics (Picard) [36mCollect whole genome sequencing-related metrics. [0m
[32m CollectRnaSeqMetrics (Picard) [36mProduces RNA alignment metrics for a SAM or BAM file. [0m
[32m CollectRrbsMetrics (Picard) [36mCollects metrics from reduced representation bisulfite sequencing (Rrbs) data. [0m
[32m CollectSamErrorMetrics (Picard) [36mProgram to collect error metrics on bases stratified in various ways.[0m
[32m CollectSequencingArtifactMetrics (Picard) [36mCollect metrics to quantify single-base sequencing artifacts. [0m
[32m CollectTargetedPcrMetrics (Picard) [36mCalculate PCR-related metrics from targeted sequencing data. [0m
[32m CollectVariantCallingMetrics (Picard) [36mCollects per-sample and aggregate (spanning all samples) metrics from the provided VCF file[0m
[32m CollectWgsMetrics (Picard) [36mCollect metrics about coverage and performance of whole genome sequencing (WGS) experiments.[0m
[32m CollectWgsMetricsWithNonZeroCoverage (Picard)[31m(EXPERIMENTAL Tool) [36mCollect metrics about coverage and performance of whole genome sequencing (WGS) experiments. [0m
[32m CompareBaseQualities [36mCompares the base qualities of two SAM/BAM/CRAM files[0m
[32m CompareDuplicatesSpark [31m(BETA Tool) [36mDetermine if two potentially identical BAMs have the same duplicate reads[0m
[32m CompareMetrics (Picard) [36mCompare two metrics files.[0m
[32m CompareSAMs (Picard) [36mCompare two input SAM/BAM/CRAM files. [0m
[32m ConvertHaplotypeDatabaseToVcf (Picard) [36mConvert Haplotype database file to vcf[0m
[32m ConvertSequencingArtifactToOxoG (Picard) [36mExtract OxoG metrics from generalized artifacts metrics. [0m
[32m CrosscheckFingerprints (Picard) [36mChecks that all data in the input files appear to have come from the same individual[0m
[32m CrosscheckReadGroupFingerprints (Picard) [36mDEPRECATED: USE CrosscheckFingerprints. [0m
[32m DumpTabixIndex [36mDumps a tabix index file.[0m
[32m EstimateLibraryComplexity (Picard) [36mEstimates the numbers of unique molecules in a sequencing library. [0m
[32m ExtractFingerprint (Picard) [36mComputes a fingerprint from the input file.[0m
[32m FlagStat [36mAccumulate flag statistics given a BAM file[0m
[32m FlagStatSpark [36mSpark tool to accumulate flag statistics[0m
[32m GatherPileupSummaries [36mCombine output files from GetPileupSummary in the order defined by a sequence dictionary[0m
[32m GetSampleName [36mEmit a single sample name[0m
[32m IdentifyContaminant (Picard) [36mComputes a fingerprint from the supplied SAM/BAM file, given a contamination estimate.[0m
[32m LiftOverHaplotypeMap (Picard) [36mLifts over a haplotype database from one reference to another[0m
[32m MeanQualityByCycle (Picard) [36mCollect mean quality by cycle.[0m
[32m MeanQualityByCycleSpark [31m(BETA Tool) [36mMeanQualityByCycle on Spark[0m
[32m QualityScoreDistribution (Picard) [36mChart the distribution of quality scores. [0m
[32m QualityScoreDistributionSpark [31m(BETA Tool) [36mQualityScoreDistribution on Spark[0m
[32m ValidateSamFile (Picard) [36mValidates a SAM/BAM/CRAM file.[0m
[32m ViewSam (Picard) [36mPrints a SAM or BAM file to the screen[0m
[37m--------------------------------------------------------------------------------------
[0m[31mExample Tools: Example tools that show developers how to implement new tools[0m
[32m ExampleMultiFeatureWalker [36mExample of a MultiFeatureWalker subclass.[0m
[32m HtsgetReader [31m(EXPERIMENTAL Tool) [36mDownload a file using htsget[0m
[37m--------------------------------------------------------------------------------------
[0m[31mFlow Based Tools: Tools designed specifically to operate on flow based data[0m
[32m CalculateAverageCombinedAnnotations [31m(EXPERIMENTAL Tool) [36mDivides annotations that were summed by genomicsDB by number of samples to calculate average.[0m
[32m FlowFeatureMapper [31m(EXPERIMENTAL Tool) [36mMap/find features in BAM file, output VCF. Initially mapping SNVs[0m
[32m GroundTruthReadsBuilder [31m(EXPERIMENTAL Tool) [36mProduces a flexible and robust ground truth set for base calling training[0m
[32m SplitCRAM [31m(EXPERIMENTAL Tool) [36mSplit CRAM files to smaller files efficiently[0m
[37m--------------------------------------------------------------------------------------
[0m[31mGenotyping Arrays Manipulation: Tools that manipulate data generated by Genotyping arrays[0m
[32m BpmToNormalizationManifestCsv (Picard) [36mProgram to convert an Illumina bpm file into a bpm.csv file.[0m
[32m CombineGenotypingArrayVcfs (Picard) [36mProgram to combine multiple genotyping array VCF files into one VCF.[0m
[32m CompareGtcFiles (Picard) [36mCompares two GTC files.[0m
[32m CreateBafRegressMetricsFile (Picard) [36mProgram to generate a picard metrics file from the output of the bafRegress tool.[0m
[32m CreateExtendedIlluminaManifest (Picard) [36mCreate an Extended Illumina Manifest for usage by the Picard tool GtcToVcf[0m
[32m CreateVerifyIDIntensityContaminationMetricsFile (Picard) [36mProgram to generate a picard metrics file from the output of the VerifyIDIntensity tool.[0m
[32m GtcToVcf (Picard) [36mProgram to convert an Illumina GTC file to a VCF[0m
[32m MergePedIntoVcf (Picard) [36mProgram to merge a single-sample ped file from zCall into a single-sample VCF.[0m
[32m VcfToAdpc (Picard) [36mProgram to convert an Arrays VCF to an ADPC file.[0m
[37m--------------------------------------------------------------------------------------
[0m[31mIntervals Manipulation: Tools that process genomic intervals in various formats[0m
[32m BedToIntervalList (Picard) [36mConverts a BED file to a Picard Interval List. [0m
[32m CompareIntervalLists [36mCompare two interval lists for equality[0m
[32m IntervalListToBed (Picard) [36mConverts an Picard IntervalList file to a BED file.[0m
[32m IntervalListTools (Picard) [36mA tool for performing various IntervalList manipulations[0m
[32m LiftOverIntervalList (Picard) [36mLifts over an interval list from one reference build to another. [0m
[32m PreprocessIntervals [36mPrepares bins for coverage collection[0m
[32m SplitIntervals [36mSplit intervals into sub-interval files.[0m
[37m--------------------------------------------------------------------------------------
[0m[31mMetagenomics: Tools that perform metagenomic analysis, e.g. microbial community composition and pathogen detection[0m
[32m PathSeqBuildKmers [36mBuilds set of host reference k-mers[0m
[32m PathSeqBuildReferenceTaxonomy [36mBuilds a taxonomy datafile of the microbe reference[0m
[32m PathSeqBwaSpark [36mStep 2: Aligns reads to the microbe reference[0m
[32m PathSeqFilterSpark [36mStep 1: Filters low quality, low complexity, duplicate, and host reads[0m
[32m PathSeqPipelineSpark [36mCombined tool that performs all steps: read filtering, microbe reference alignment, and abundance scoring[0m
[32m PathSeqScoreSpark [36mStep 3: Classifies pathogen-aligned reads and generates abundance scores[0m
[37m--------------------------------------------------------------------------------------
[0m[31mMethylation-Specific Tools: Tools that perform methylation calling, processing bisulfite sequenced, methylation-aware aligned BAM[0m
[32m MethylationTypeCaller [31m(EXPERIMENTAL Tool) [36mIdentify methylated bases from bisulfite sequenced, methylation-aware BAMs[0m
[37m--------------------------------------------------------------------------------------
[0m[31mOther: Miscellaneous tools, e.g. those that aid in data streaming[0m
[32m CreateHadoopBamSplittingIndex [31m(BETA Tool) [36mCreate a Hadoop BAM splitting index[0m
[32m FifoBuffer (Picard) [36mProvides a large, FIFO buffer that can be used to buffer input and output streams between programs.[0m
[32m GatherBQSRReports [36mGathers scattered BQSR recalibration reports into a single file[0m
[32m GatherTranches [31m(BETA Tool) [36mGathers scattered VQSLOD tranches into a single file[0m
[32m IndexFeatureFile [36mCreates an index for a feature file, e.g. VCF or BED file.[0m
[32m ParallelCopyGCSDirectoryIntoHDFSSpark [31m(BETA Tool) [36mParallel copy a file or directory from Google Cloud Storage into the HDFS file system used by Spark[0m
[32m PrintBGZFBlockInformation [31m(EXPERIMENTAL Tool) [36mPrint information about the compressed blocks in a BGZF format file[0m
[32m ReadAnonymizer [31m(EXPERIMENTAL Tool) [36mReplace bases in reads with reference bases.[0m
[32m ReblockGVCF [36mCondenses homRef blocks in a single-sample GVCF[0m
[32m SortGff (Picard) [36mSorts a gff3 file, and adds flush directives[0m
[37m--------------------------------------------------------------------------------------
[0m[31mRead Data Manipulation: Tools that manipulate read data in SAM, BAM or CRAM format[0m
[32m AddCommentsToBam (Picard) [36mAdds comments to the header of a BAM file.[0m
[32m AddOATag (Picard) [36mRecord current alignment information to OA tag.[0m
[32m AddOrReplaceReadGroups (Picard) [36mAssigns all the reads in a file to a single new read-group.[0m
[32m AddOriginalAlignmentTags [31m(EXPERIMENTAL Tool) [36mAdds Original Alignment tag and original mate contig tag[0m
[32m ApplyBQSR [36mApply base quality score recalibration[0m
[32m ApplyBQSRSpark [31m(BETA Tool) [36mApply base quality score recalibration on Spark[0m
[32m BQSRPipelineSpark [31m(BETA Tool) [36mBoth steps of BQSR (BaseRecalibrator and ApplyBQSR) on Spark[0m
[32m BamToBfq (Picard) [36mConverts a BAM file into a BFQ (binary fastq formatted) file[0m
[32m BaseRecalibrator [36mGenerates recalibration table for Base Quality Score Recalibration (BQSR)[0m
[32m BaseRecalibratorSpark [31m(BETA Tool) [36mGenerate recalibration table for Base Quality Score Recalibration (BQSR) on Spark[0m
[32m BuildBamIndex (Picard) [36mGenerates a BAM index ".bai" file. [0m
[32m BwaAndMarkDuplicatesPipelineSpark [31m(BETA Tool) [36mTakes name-sorted file and runs BWA and MarkDuplicates.[0m
[32m BwaSpark [31m(BETA Tool) [36mAlign reads to a given reference using BWA on Spark[0m
[32m CleanSam (Picard) [36mCleans a SAM/BAM/CRAM files, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads[0m
[32m ClipReads [36mClip reads in a SAM/BAM/CRAM file[0m
[32m CollectDuplicateMetrics (Picard) [36mCollect Duplicate metrics from marked file.[0m
[32m ConvertHeaderlessHadoopBamShardToBam [31m(BETA Tool) [36mConvert a headerless BAM shard into a readable BAM[0m
[32m DownsampleByDuplicateSet [31m(BETA Tool) [36mDiscard a set fraction of duplicate sets from a UMI-grouped bam[0m
[32m DownsampleSam (Picard) [36mDownsample a SAM or BAM file.[0m
[32m ExtractOriginalAlignmentRecordsByNameSpark [31m(BETA Tool) [36mSubsets reads by name[0m
[32m FastqToSam (Picard) [36mConverts a FASTQ file to an unaligned BAM or SAM file[0m
[32m FilterSamReads (Picard) [36mSubsets reads from a SAM/BAM/CRAM file by applying one of several filters.[0m
[32m FixMateInformation (Picard) [36mVerify mate-pair information between mates and fix if needed.[0m
[32m FixMisencodedBaseQualityReads [36mFix Illumina base quality scores in a SAM/BAM/CRAM file[0m
[32m GatherBamFiles (Picard) [36mConcatenate efficiently BAM files that resulted from a scattered parallel analysis[0m
[32m LeftAlignIndels [36mLeft-aligns indels from reads in a SAM/BAM/CRAM file[0m
[32m MarkDuplicates (Picard) [36mIdentifies duplicate reads. [0m
[32m MarkDuplicatesSpark [36mMarkDuplicates on Spark[0m
[32m MarkDuplicatesWithMateCigar (Picard) [36mIdentifies duplicate reads, accounting for mate CIGAR. [0m
[32m MergeBamAlignment (Picard) [36mMerge alignment data from a SAM or BAM with data in an unmapped BAM file. [0m
[32m MergeSamFiles (Picard) [36mMerges multiple SAM/BAM/CRAM (and/or) files into a single file. [0m
[32m PositionBasedDownsampleSam (Picard) [36mDownsample a SAM or BAM file to retain a subset of the reads based on the reads location in each tile in the flowcell.[0m
[32m PostProcessReadsForRSEM [31m(BETA Tool) [36mReorder reads before running RSEM[0m
[32m PrintDistantMates [36mUnmaps reads with distant mates.[0m
[32m PrintReads [36mPrint reads in the SAM/BAM/CRAM file[0m
[32m PrintReadsHeader [36mPrint the header from a SAM/BAM/CRAM file[0m
[32m PrintReadsSpark [36mPrintReads on Spark[0m
[32m ReorderSam (Picard) [36mReorders reads in a SAM or BAM file to match ordering in a second reference file.[0m
[32m ReplaceSamHeader (Picard) [36mReplaces the SAMFileHeader in a SAM/BAM/CRAM file. [0m
[32m RevertBaseQualityScores [36mRevert Quality Scores in a SAM/BAM/CRAM file[0m
[32m RevertOriginalBaseQualitiesAndAddMateCigar (Picard)[36mReverts the original base qualities and adds the mate cigar tag to read-group files[0m
[32m RevertSam (Picard) [36mReverts SAM/BAM/CRAM files to a previous state. [0m
[32m RevertSamSpark [31m(BETA Tool) [36mReverts SAM, BAM or CRAM files to a previous state.[0m
[32m SamFormatConverter (Picard) [36mConvert a BAM file to a SAM file, or a SAM to a BAM[0m
[32m SamToFastq (Picard) [36mConverts a SAM/BAM/CRAM file to FASTQ.[0m
[32m SamToFastqWithTags (Picard) [36mConverts a SAM or BAM file to FASTQ alongside FASTQs created from tags.[0m
[32m SetNmAndUqTags (Picard) [36mDEPRECATED: Use SetNmMdAndUqTags instead.[0m
[32m SetNmMdAndUqTags (Picard) [36mFixes the NM, MD, and UQ tags in a SAM/BAM/CRAM file [0m
[32m SimpleMarkDuplicatesWithMateCigar (Picard) [31m(EXPERIMENTAL Tool) [36mExamines aligned records in the supplied SAM or BAM file to locate duplicate molecules.[0m
[32m SortSam (Picard) [36mSorts a SAM, BAM or CRAM file. [0m
[32m SortSamSpark [31m(BETA Tool) [36mSortSam on Spark (works on SAM/BAM/CRAM)[0m
[32m SplitNCigarReads [36mSplit Reads with N in Cigar[0m
[32m SplitReads [36mOutputs reads from a SAM/BAM/CRAM by read group, sample and library name[0m
[32m SplitSamByLibrary (Picard) [36mSplits a SAM/BAM/CRAM file into individual files by library[0m
[32m SplitSamByNumberOfReads (Picard) [36mSplits a SAM/BAM/CRAM file to multiple files.[0m
[32m TransferReadTags [31m(EXPERIMENTAL Tool) [36mIncorporate read tags in a SAM file to that of a matching SAM file[0m
[32m UmiAwareMarkDuplicatesWithMateCigar (Picard) [31m(EXPERIMENTAL Tool) [36mIdentifies duplicate reads using information from read positions and UMIs. [0m
[32m UnmarkDuplicates [36mClears the 0x400 duplicate SAM flag[0m
[37m--------------------------------------------------------------------------------------
[0m[31mReference: Tools that analyze and manipulate FASTA format references[0m
[32m BaitDesigner (Picard) [36mDesigns oligonucleotide baits for hybrid selection reactions.[0m
[32m BwaMemIndexImageCreator [36mCreate a BWA-MEM index image file for use with GATK BWA tools[0m
[32m CheckReferenceCompatibility [31m(EXPERIMENTAL Tool) [36mCheck a BAM/VCF for compatibility against specified references.[0m
[32m CompareReferences [31m(EXPERIMENTAL Tool) [36mDisplay reference comparison as a tab-delimited table and summarize reference differences.[0m
[32m ComposeSTRTableFile [36mComposes a genome-wide STR location table used for DragSTR model auto-calibration[0m
[32m CountBasesInReference [36mCount the numbers of each base in a reference file[0m
[32m CreateSequenceDictionary (Picard) [36mCreates a sequence dictionary for a reference sequence. [0m
[32m ExtractSequences (Picard) [36mSubsets intervals from a reference sequence to a new FASTA file.[0m
[32m FastaAlternateReferenceMaker [36mCreate an alternative reference by combining a fasta with a vcf.[0m
[32m FastaReferenceMaker [36mCreate snippets of a fasta file[0m
[32m FindBadGenomicKmersSpark [31m(BETA Tool) [36mIdentifies sequences that occur at high frequency in a reference[0m
[32m NonNFastaSize (Picard) [36mCounts the number of non-N bases in a fasta file.[0m
[32m NormalizeFasta (Picard) [36mNormalizes lines of sequence in a FASTA file to be of the same length.[0m
[32m ScatterIntervalsByNs (Picard) [36mWrites an interval list created by splitting a reference at Ns.[0m
[32m ShiftFasta [31m(BETA Tool) [36mCreates a shifted fasta file and shift_back file[0m
[37m--------------------------------------------------------------------------------------
[0m[31mShort Variant Discovery: Tools that perform variant calling and genotyping for short variants (SNPs, SNVs and Indels)[0m
[32m CalibrateDragstrModel [36mestimates the parameters for the DRAGstr model[0m
[32m CombineGVCFs [36mMerges one or more HaplotypeCaller GVCF files into a single GVCF with appropriate annotations[0m
[32m GenomicsDBImport [36mImport VCFs to GenomicsDB[0m
[32m GenotypeGVCFs [36mPerform joint genotyping on one or more samples pre-called with HaplotypeCaller[0m
[32m GnarlyGenotyper [31m(BETA Tool) [36mPerform "quick and dirty" joint genotyping on one or more samples pre-called with HaplotypeCaller[0m
[32m HaplotypeBasedVariantRecaller [31m(EXPERIMENTAL Tool) [36mCalculate likelihood matrix for each Allele in VCF against a set of Reads limited by a set of Haplotypes[0m
[32m HaplotypeCaller [36mCall germline SNPs and indels via local re-assembly of haplotypes[0m
[32m HaplotypeCallerSpark [31m(BETA Tool) [36mHaplotypeCaller on Spark[0m
[32m LearnReadOrientationModel [36mGet the maximum likelihood estimates of artifact prior probabilities in the orientation bias mixture model filter[0m
[32m MergeMutectStats [36mMerge the stats output by scatters of a single Mutect2 job[0m
[32m Mutect2 [36mCall somatic SNVs and indels via local assembly of haplotypes[0m
[32m RampedHaplotypeCaller [31m(EXPERIMENTAL Tool) [36mCall germline SNPs and indels via local re-assembly of haplotypes (ramped version)[0m
[32m ReadsPipelineSpark [31m(BETA Tool) [36mRuns BWA (if specified), MarkDuplicates, BQSR, and HaplotypeCaller on unaligned or aligned reads to generate a VCF.[0m
[37m--------------------------------------------------------------------------------------
[0m[31mStructural Variant Discovery: Tools that detect structural variants [0m
[32m CollectSVEvidence [31m(BETA Tool) [36mGathers paired-end and split read evidence files for use in the GATK-SV pipeline.[0m
[32m CondenseDepthEvidence [31m(EXPERIMENTAL Tool) [36mMerges adjacent DepthEvidence records.[0m
[32m CpxVariantReInterpreterSpark [31m(BETA Tool) [36m(Internal) Tries to extract simple variants from a provided GATK-SV CPX.vcf[0m
[32m DiscoverVariantsFromContigAlignmentsSAMSpark [31m(BETA Tool) [36m(Internal) Examines aligned contigs from local assemblies and calls structural variants[0m
[32m ExtractSVEvidenceSpark [31m(BETA Tool) [36m(Internal) Extracts evidence of structural variations from reads[0m
[32m FindBreakpointEvidenceSpark [31m(BETA Tool) [36m(Internal) Produces local assemblies of genomic regions that may harbor structural variants[0m
[32m JointGermlineCNVSegmentation [31m(BETA Tool) [36mCombine segmented gCNV VCFs.[0m
[32m PrintReadCounts [31m(EXPERIMENTAL Tool) [36mPrints count files for CNV determination.[0m
[32m PrintSVEvidence [31m(EXPERIMENTAL Tool) [36mMerges SV evidence records.[0m
[32m SVAnnotate [36mAdds gene overlap and variant consequence annotations to SV VCF from GATK-SV pipeline[0m
[32m SVCluster [31m(BETA Tool) [36mClusters structural variants[0m
[32m SiteDepthtoBAF [31m(EXPERIMENTAL Tool) [36mConvert SiteDepth to BafEvidence[0m
[32m StructuralVariantDiscoverer [31m(BETA Tool) [36m(Internal) Examines aligned contigs from local assemblies and calls structural variants or their breakpoints[0m
[32m StructuralVariationDiscoveryPipelineSpark [31m(BETA Tool) [36mRuns the structural variation discovery workflow on a single sample[0m
[32m SvDiscoverFromLocalAssemblyContigAlignmentsSpark [31m(BETA Tool) [36m(Internal) Examines aligned contigs from local assemblies and calls structural variants or their breakpoints[0m
[37m--------------------------------------------------------------------------------------
[0m[31mVariant Evaluation and Refinement: Tools that evaluate and refine variant calls, e.g. with annotations not offered by the engine[0m
[32m AlleleFrequencyQC [31m(BETA Tool) [36mGeneral-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more)[0m
[32m AnnotateVcfWithBamDepth [36m(Internal) Annotate a vcf with a bam's read depth at each variant locus[0m
[32m AnnotateVcfWithExpectedAlleleFraction [36m(Internal) Annotate a vcf with expected allele fractions in pooled sequencing[0m
[32m CalculateGenotypePosteriors [36mCalculate genotype posterior probabilities given family and/or known population genotypes[0m
[32m CalculateMixingFractions [36m(Internal) Calculate proportions of different samples in a pooled bam[0m
[32m Concordance [36mEvaluate concordance of an input VCF against a validated truth VCF[0m
[32m CountFalsePositives [31m(BETA Tool) [36mCount PASS variants[0m
[32m CountVariants [36mCounts variant records in a VCF file, regardless of filter status.[0m
[32m CountVariantsSpark [36mCountVariants on Spark[0m
[32m EvaluateInfoFieldConcordance [31m(BETA Tool) [36mEvaluate concordance of info fields in an input VCF against a validated truth VCF[0m
[32m FilterFuncotations [31m(EXPERIMENTAL Tool) [36mFilter variants based on clinically-significant Funcotations.[0m
[32m FindMendelianViolations (Picard) [36mFinds mendelian violations of all types within a VCF[0m
[32m FuncotateSegments [31m(BETA Tool) [36mFunctional annotation for segment files. The output formats are not well-defined and subject to change.[0m
[32m Funcotator [36mFunctional Annotator[0m
[32m FuncotatorDataSourceDownloader [36mData source downloader for Funcotator.[0m
[32m GenotypeConcordance (Picard) [36mCalculates the concordance between genotype data of one sample in each of two VCFs - truth (or reference) vs. calls.[0m
[32m MergeMutect2CallsWithMC3 [31m(EXPERIMENTAL Tool) [36mUNSUPPORTED. FOR EVALUATION ONLY. Merge M2 calls with MC[0m
[32m ReferenceBlockConcordance [36mEvaluate GVCF reference block concordance of an input GVCF against a truth GVCF[0m
[32m ValidateBasicSomaticShortMutations [31m(EXPERIMENTAL Tool) [36mCheck variants against tumor-normal bams representing the same samples, though not the ones from the actual calls.[0m
[32m ValidateVariants [36mValidate VCF[0m
[32m VariantEval [31m(BETA Tool) [36mGeneral-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more)[0m
[32m VariantsToTable [36mExtract fields from a VCF file to a tab-delimited table[0m
[37m--------------------------------------------------------------------------------------
[0m[31mVariant Filtering: Tools that filter variants by annotating the FILTER column[0m
[32m ApplyVQSR [36m Apply a score cutoff to filter variants based on a recalibration table[0m
[32m CNNScoreVariants [36mApply a Convolutional Neural Net to filter annotated variants[0m
[32m CNNVariantTrain [31m(EXPERIMENTAL Tool) [36mTrain a CNN model for filtering variants[0m
[32m CNNVariantWriteTensors [31m(EXPERIMENTAL Tool) [36mWrite variant tensors for training a CNN to filter variants[0m
[32m CreateSomaticPanelOfNormals [31m(BETA Tool) [36mMake a panel of normals for use with Mutect2[0m
[32m ExtractVariantAnnotations [31m(BETA Tool) [36mExtracts site-level variant annotations, labels, and other metadata from a VCF file to HDF5 files[0m
[32m FilterAlignmentArtifacts [31m(EXPERIMENTAL Tool) [36mFilter alignment artifacts from a vcf callset.[0m
[32m FilterMutectCalls [36mFilter somatic SNVs and indels called by Mutect2[0m
[32m FilterVariantTranches [36mApply tranche filtering[0m
[32m FilterVcf (Picard) [36mHard filters a VCF.[0m
[32m MTLowHeteroplasmyFilterTool [36mIf too many low het sites, filter all low het sites[0m
[32m NuMTFilterTool [36mUses the median autosomal coverage and the allele depth to determine whether the allele might be a NuMT[0m
[32m ScoreVariantAnnotations [31m(BETA Tool) [36mScores variant calls in a VCF file based on site-level annotations using a previously trained model[0m
[32m TrainVariantAnnotationsModel [31m(BETA Tool) [36mTrains a model for scoring variant calls based on site-level annotations[0m
[32m VariantFiltration [36mFilter variant calls based on INFO and/or FORMAT annotations[0m
[32m VariantRecalibrator [36mBuild a recalibration model to score variant quality for filtering purposes[0m
[37m--------------------------------------------------------------------------------------
[0m[31mVariant Manipulation: Tools that manipulate variant call format (VCF) data[0m
[32m FixVcfHeader (Picard) [36mReplaces or fixes a VCF header.[0m
[32m GatherVcfs (Picard) [36mGathers multiple VCF files from a scatter operation into a single VCF file[0m
[32m GatherVcfsCloud [31m(BETA Tool) [36mGathers multiple VCF files from a scatter operation into a single VCF file[0m
[32m LeftAlignAndTrimVariants [36mLeft align and trim vairants[0m
[32m LiftoverVcf (Picard) [36mLifts over a VCF file from one reference build to another. [0m
[32m MakeSitesOnlyVcf (Picard) [36mCreates a VCF that contains all the site-level information for all records in the input VCF but no genotype information.[0m
[32m MakeVcfSampleNameMap (Picard) [36mCreates a TSV from sample name to VCF/GVCF path, with one line per input.[0m
[32m MergeVcfs (Picard) [36mCombines multiple variant files into a single variant file[0m
[32m PrintVariantsSpark [36mPrints out variants from the input VCF.[0m
[32m RemoveNearbyIndels [36m(Internal) Remove indels from the VCF file that are close to each other.[0m
[32m RenameSampleInVcf (Picard) [36mRenames a sample within a VCF or BCF.[0m
[32m SelectVariants [36mSelect a subset of variants from a VCF file[0m
[32m SortVcf (Picard) [36mSorts one or more VCF files. [0m
[32m SplitVcfs (Picard) [36mSplits SNPs and INDELs into separate files. [0m
[32m UpdateVCFSequenceDictionary [36mUpdates the sequence dictionary in a variant file.[0m
[32m UpdateVcfSequenceDictionary (Picard) [36mTakes a VCF and a second file that contains a sequence dictionary and updates the VCF with the new sequence dictionary.[0m
[32m VariantAnnotator [36mTool for adding annotations to VCF files[0m
[32m VcfFormatConverter (Picard) [36mConverts VCF to BCF or BCF to VCF. [0m
[32m VcfToIntervalList (Picard) [36mConverts a VCF or BCF file to a Picard Interval List[0m
[37m--------------------------------------------------------------------------------------
[0m
***********************************************************************
A USER ERROR has occurred: '-Xmx104857M' is not a valid command.
***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
Using GATK jar /gatk/gatk-package-4.3.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /gatk/gatk-package-4.3.0.0-local.jar -Xmx104857M SplitNCigarReads -R input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta -I output.temp/Le1-12-501-708_1.fastq.gz_addrg_repN.bam -O output2/Le1-12-501-708_1.fastq.gz.bam
/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
INFO 2023-02-28 23:40:41 AddOrReplaceReadGroups
********** NOTE: Picard's command line syntax is changing.
**********
********** For more information, please see:
********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
**********
********** The command line looks like this in the new syntax:
**********
********** AddOrReplaceReadGroups -I output/Le1-13-502-701_1.fastq.gz.bam -O output.temp/Le1-13-502-701_1.fastq.gz_addrg.bam -SO coordinate -RGID Le1-13-502-701_1.fastq.gz -RGLB library -RGPL Illumina -RGPU Illumina -RGSM Le1-13-502-701_1.fastq.gz
**********
23:40:41.719 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/picard-2.18.27-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Tue Feb 28 23:40:41 GMT 2023] AddOrReplaceReadGroups INPUT=output/Le1-13-502-701_1.fastq.gz.bam OUTPUT=output.temp/Le1-13-502-701_1.fastq.gz_addrg.bam SORT_ORDER=coordinate RGID=Le1-13-502-701_1.fastq.gz RGLB=library RGPL=Illumina RGPU=Illumina RGSM=Le1-13-502-701_1.fastq.gz VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Tue Feb 28 23:40:41 GMT 2023] Executing as ?@9dff24c3b9b6 on Linux 3.10.0-1160.36.2.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.27-SNAPSHOT
INFO 2023-02-28 23:40:41 AddOrReplaceReadGroups Created read-group ID=Le1-13-502-701_1.fastq.gz PL=Illumina LB=library SM=Le1-13-502-701_1.fastq.gz
[Tue Feb 28 23:40:47 GMT 2023] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=2600468480
[1m[31mUSAGE: [32m[1m[31m [-h]
[0m[1m[31mAvailable Programs:
[0m[37m--------------------------------------------------------------------------------------
[0m[31mBase Calling: Tools that process sequencing machine data, e.g. Illumina base calls, and detect sequencing level attributes, e.g. adapters[0m
[32m CheckIlluminaDirectory (Picard) [36mAsserts the validity for specified Illumina basecalling data. [0m
[32m CollectIlluminaBasecallingMetrics (Picard) [36mCollects Illumina Basecalling metrics for a sequencing run. [0m
[32m CollectIlluminaLaneMetrics (Picard) [36mCollects Illumina lane metrics for the given BaseCalling analysis directory.[0m
[32m ExtractIlluminaBarcodes (Picard) [36mTool determines the barcode for each read in an Illumina lane. [0m
[32m IlluminaBasecallsToFastq (Picard) [36mGenerate FASTQ file(s) from Illumina basecall read data. [0m
[32m IlluminaBasecallsToSam (Picard) [36mTransforms raw Illumina sequencing data into an unmapped SAM, BAM or CRAM file.[0m
[32m MarkIlluminaAdapters (Picard) [36mReads a SAM/BAM/CRAM file and rewrites it with new adapter-trimming tags. [0m
[37m--------------------------------------------------------------------------------------
[0m[31mCopy Number Variant Discovery: Tools that analyze read coverage to detect copy number variants.[0m
[32m AnnotateIntervals [36mAnnotates intervals with GC content, mappability, and segmental-duplication content[0m
[32m CallCopyRatioSegments [36mCalls copy-ratio segments as amplified, deleted, or copy-number neutral[0m
[32m CombineSegmentBreakpoints [31m(EXPERIMENTAL Tool) [36mCombine the breakpoints of two segment files and annotate the resulting intervals with chosen columns from each file.[0m
[32m CreateReadCountPanelOfNormals [36mCreates a panel of normals for read-count denoising[0m
[32m DenoiseReadCounts [36mDenoises read counts to produce denoised copy ratios[0m
[32m DetermineGermlineContigPloidy [36mDetermines the baseline contig ploidy for germline samples given counts data[0m
[32m FilterIntervals [36mFilters intervals based on annotations and/or count statistics[0m
[32m GermlineCNVCaller [36mCalls copy-number variants in germline samples given their counts and the output of DetermineGermlineContigPloidy[0m
[32m MergeAnnotatedRegions [31m(EXPERIMENTAL Tool) [36mMerge annotated genomic regions based entirely on touching/overlapping intervals.[0m
[32m MergeAnnotatedRegionsByAnnotation [31m(EXPERIMENTAL Tool) [36mMerge annotated genomic regions within specified distance if annotation value(s) are exactly the same.[0m
[32m ModelSegments [36mModels segmented copy ratios from denoised copy ratios and segmented minor-allele fractions from allelic counts[0m
[32m PlotDenoisedCopyRatios [36mCreates plots of denoised copy ratios[0m
[32m PlotModeledSegments [36mCreates plots of denoised and segmented copy-ratio and minor-allele-fraction estimates[0m
[32m PostprocessGermlineCNVCalls [36mPostprocesses the output of GermlineCNVCaller and generates VCFs and denoised copy ratios[0m
[32m TagGermlineEvents [31m(EXPERIMENTAL Tool) [36mDo a simplistic tagging of germline events in a tumor segment file.[0m
[37m--------------------------------------------------------------------------------------
[0m[31mCoverage Analysis: Tools that count coverage, e.g. depth per allele[0m
[32m ASEReadCounter [36mGenerates table of filtered base counts at het sites for allele specific expression[0m
[32m AnalyzeSaturationMutagenesis [31m(BETA Tool) [36m(EXPERIMENTAL) Processes reads from a MITESeq or other saturation mutagenesis experiment.[0m
[32m CollectAllelicCounts [36mCollects reference and alternate allele counts at specified sites[0m
[32m CollectAllelicCountsSpark [36mCollects reference and alternate allele counts at specified sites[0m
[32m CollectF1R2Counts [36mCollect F1R2 read counts for the Mutect2 orientation bias mixture model filter[0m
[32m CollectReadCounts [36mCollects read counts at specified intervals[0m
[32m CountBases [36mCount bases in a SAM/BAM/CRAM file[0m
[32m CountBasesSpark [36mCounts bases in the input SAM/BAM[0m
[32m CountReads [36mCount reads in a SAM/BAM/CRAM file[0m
[32m CountReadsSpark [36mCounts reads in the input SAM/BAM[0m
[32m DepthOfCoverage [31m(BETA Tool) [36mGenerate coverage summary information for reads data[0m
[32m GatherNormalArtifactData [36mCombine output files from GetNormalArtifactData in the order defined by a sequence dictionary[0m
[32m GeneExpressionEvaluation [31m(BETA Tool) [36mEvaluate gene expression from RNA-seq reads aligned to genome.[0m
[32m GetNormalArtifactData [36mCollects data for training normal artifact filter[0m
[32m GetPileupSummaries [36mTabulates pileup metrics for inferring contamination[0m
[32m LocalAssembler [31m(BETA Tool) [36mLocal assembler for SVs[0m
[32m Pileup [36mPrints read alignments in samtools pileup format[0m
[32m PileupSpark [31m(BETA Tool) [36mPrints read alignments in samtools pileup format[0m
[37m--------------------------------------------------------------------------------------
[0m[31mDiagnostics and Quality Control: Tools that collect sequencing quality related and comparative metrics[0m
[32m AccumulateQualityYieldMetrics (Picard) [36mCombines multiple QualityYieldMetrics files into a single file.[0m
[32m AccumulateVariantCallingMetrics (Picard) [36mCombines multiple Variant Calling Metrics files into a single file[0m
[32m AnalyzeCovariates [36mEvaluate and compare base quality score recalibration (BQSR) tables[0m
[32m BamIndexStats (Picard) [36mGenerate index statistics from a BAM file[0m
[32m CalcMetadataSpark [31m(BETA Tool) [36m(Internal) Collects read metrics relevant to structural variant discovery[0m
[32m CalculateContamination [36mCalculate the fraction of reads coming from cross-sample contamination[0m
[32m CalculateFingerprintMetrics (Picard) [36mCalculate statistics on fingerprints, checking their viability[0m
[32m CalculateReadGroupChecksum (Picard) [36mCreates a hash code based on the read groups (RG). [0m
[32m CheckDuplicateMarking (Picard) [36mChecks the consistency of duplicate markings.[0m
[32m CheckFingerprint (Picard) [36mComputes a fingerprint from the supplied input (SAM/BAM/CRAM or VCF) file and compares it to the provided genotypes[0m
[32m CheckPileup [36mCompare GATK's internal pileup to a reference Samtools mpileup[0m
[32m CheckTerminatorBlock (Picard) [36mAsserts the provided gzip file's (e.g., BAM) last block is well-formed; RC 100 otherwise[0m
[32m ClusterCrosscheckMetrics (Picard) [36mClusters the results of a CrosscheckFingerprints run by LOD score[0m
[32m CollectAlignmentSummaryMetrics (Picard) [36mProduces a summary of alignment metrics from a SAM or BAM file. [0m
[32m CollectArraysVariantCallingMetrics (Picard) [36mCollects summary and per-sample from the provided arrays VCF file[0m
[32m CollectBaseDistributionByCycle (Picard) [36mChart the nucleotide distribution per cycle in a SAM or BAM file[0m
[32m CollectBaseDistributionByCycleSpark [31m(BETA Tool) [36mCollects base distribution per cycle in SAM/BAM/CRAM file(s).[0m
[32m CollectGcBiasMetrics (Picard) [36mCollect metrics regarding GC bias. [0m
[32m CollectHiSeqXPfFailMetrics (Picard) [36mClassify PF-Failing reads in a HiSeqX Illumina Basecalling directory into various categories.[0m
[32m CollectHsMetrics (Picard) [36mCollects hybrid-selection (HS) metrics for a SAM or BAM file. [0m
[32m CollectIndependentReplicateMetrics (Picard) [31m(EXPERIMENTAL Tool) [36mEstimates the rate of independent replication rate of reads within a bam.
[0m
[32m CollectInsertSizeMetrics (Picard) [36mCollect metrics about the insert size distribution of a paired-end library. [0m
[32m CollectInsertSizeMetricsSpark [31m(BETA Tool) [36mCollects insert size distribution information on alignment data[0m
[32m CollectJumpingLibraryMetrics (Picard) [36mCollect jumping library metrics. [0m
[32m CollectMultipleMetrics (Picard) [36mCollect multiple classes of metrics. [0m
[32m CollectMultipleMetricsSpark [31m(BETA Tool) [36mRuns multiple metrics collection modules for a given alignment file[0m
[32m CollectOxoGMetrics (Picard) [36mCollect metrics to assess oxidative artifacts.[0m
[32m CollectQualityYieldMetrics (Picard) [36mCollect metrics about reads that pass quality thresholds and Illumina-specific filters. [0m
[32m CollectQualityYieldMetricsSpark [31m(BETA Tool) [36mCollects quality yield metrics from SAM/BAM/CRAM file(s).[0m
[32m CollectRawWgsMetrics (Picard) [36mCollect whole genome sequencing-related metrics. [0m
[32m CollectRnaSeqMetrics (Picard) [36mProduces RNA alignment metrics for a SAM or BAM file. [0m
[32m CollectRrbsMetrics (Picard) [36mCollects metrics from reduced representation bisulfite sequencing (Rrbs) data. [0m
[32m CollectSamErrorMetrics (Picard) [36mProgram to collect error metrics on bases stratified in various ways.[0m
[32m CollectSequencingArtifactMetrics (Picard) [36mCollect metrics to quantify single-base sequencing artifacts. [0m
[32m CollectTargetedPcrMetrics (Picard) [36mCalculate PCR-related metrics from targeted sequencing data. [0m
[32m CollectVariantCallingMetrics (Picard) [36mCollects per-sample and aggregate (spanning all samples) metrics from the provided VCF file[0m
[32m CollectWgsMetrics (Picard) [36mCollect metrics about coverage and performance of whole genome sequencing (WGS) experiments.[0m
[32m CollectWgsMetricsWithNonZeroCoverage (Picard)[31m(EXPERIMENTAL Tool) [36mCollect metrics about coverage and performance of whole genome sequencing (WGS) experiments. [0m
[32m CompareBaseQualities [36mCompares the base qualities of two SAM/BAM/CRAM files[0m
[32m CompareDuplicatesSpark [31m(BETA Tool) [36mDetermine if two potentially identical BAMs have the same duplicate reads[0m
[32m CompareMetrics (Picard) [36mCompare two metrics files.[0m
[32m CompareSAMs (Picard) [36mCompare two input SAM/BAM/CRAM files. [0m
[32m ConvertHaplotypeDatabaseToVcf (Picard) [36mConvert Haplotype database file to vcf[0m
[32m ConvertSequencingArtifactToOxoG (Picard) [36mExtract OxoG metrics from generalized artifacts metrics. [0m
[32m CrosscheckFingerprints (Picard) [36mChecks that all data in the input files appear to have come from the same individual[0m
[32m CrosscheckReadGroupFingerprints (Picard) [36mDEPRECATED: USE CrosscheckFingerprints. [0m
[32m DumpTabixIndex [36mDumps a tabix index file.[0m
[32m EstimateLibraryComplexity (Picard) [36mEstimates the numbers of unique molecules in a sequencing library. [0m
[32m ExtractFingerprint (Picard) [36mComputes a fingerprint from the input file.[0m
[32m FlagStat [36mAccumulate flag statistics given a BAM file[0m
[32m FlagStatSpark [36mSpark tool to accumulate flag statistics[0m
[32m GatherPileupSummaries [36mCombine output files from GetPileupSummary in the order defined by a sequence dictionary[0m
[32m GetSampleName [36mEmit a single sample name[0m
[32m IdentifyContaminant (Picard) [36mComputes a fingerprint from the supplied SAM/BAM file, given a contamination estimate.[0m
[32m LiftOverHaplotypeMap (Picard) [36mLifts over a haplotype database from one reference to another[0m
[32m MeanQualityByCycle (Picard) [36mCollect mean quality by cycle.[0m
[32m MeanQualityByCycleSpark [31m(BETA Tool) [36mMeanQualityByCycle on Spark[0m
[32m QualityScoreDistribution (Picard) [36mChart the distribution of quality scores. [0m
[32m QualityScoreDistributionSpark [31m(BETA Tool) [36mQualityScoreDistribution on Spark[0m
[32m ValidateSamFile (Picard) [36mValidates a SAM/BAM/CRAM file.[0m
[32m ViewSam (Picard) [36mPrints a SAM or BAM file to the screen[0m
[37m--------------------------------------------------------------------------------------
[0m[31mExample Tools: Example tools that show developers how to implement new tools[0m
[32m ExampleMultiFeatureWalker [36mExample of a MultiFeatureWalker subclass.[0m
[32m HtsgetReader [31m(EXPERIMENTAL Tool) [36mDownload a file using htsget[0m
[37m--------------------------------------------------------------------------------------
[0m[31mFlow Based Tools: Tools designed specifically to operate on flow based data[0m
[32m CalculateAverageCombinedAnnotations [31m(EXPERIMENTAL Tool) [36mDivides annotations that were summed by genomicsDB by number of samples to calculate average.[0m
[32m FlowFeatureMapper [31m(EXPERIMENTAL Tool) [36mMap/find features in BAM file, output VCF. Initially mapping SNVs[0m
[32m GroundTruthReadsBuilder [31m(EXPERIMENTAL Tool) [36mProduces a flexible and robust ground truth set for base calling training[0m
[32m SplitCRAM [31m(EXPERIMENTAL Tool) [36mSplit CRAM files to smaller files efficiently[0m
[37m--------------------------------------------------------------------------------------
[0m[31mGenotyping Arrays Manipulation: Tools that manipulate data generated by Genotyping arrays[0m
[32m BpmToNormalizationManifestCsv (Picard) [36mProgram to convert an Illumina bpm file into a bpm.csv file.[0m
[32m CombineGenotypingArrayVcfs (Picard) [36mProgram to combine multiple genotyping array VCF files into one VCF.[0m
[32m CompareGtcFiles (Picard) [36mCompares two GTC files.[0m
[32m CreateBafRegressMetricsFile (Picard) [36mProgram to generate a picard metrics file from the output of the bafRegress tool.[0m
[32m CreateExtendedIlluminaManifest (Picard) [36mCreate an Extended Illumina Manifest for usage by the Picard tool GtcToVcf[0m
[32m CreateVerifyIDIntensityContaminationMetricsFile (Picard) [36mProgram to generate a picard metrics file from the output of the VerifyIDIntensity tool.[0m
[32m GtcToVcf (Picard) [36mProgram to convert an Illumina GTC file to a VCF[0m
[32m MergePedIntoVcf (Picard) [36mProgram to merge a single-sample ped file from zCall into a single-sample VCF.[0m
[32m VcfToAdpc (Picard) [36mProgram to convert an Arrays VCF to an ADPC file.[0m
[37m--------------------------------------------------------------------------------------
[0m[31mIntervals Manipulation: Tools that process genomic intervals in various formats[0m
[32m BedToIntervalList (Picard) [36mConverts a BED file to a Picard Interval List. [0m
[32m CompareIntervalLists [36mCompare two interval lists for equality[0m
[32m IntervalListToBed (Picard) [36mConverts an Picard IntervalList file to a BED file.[0m
[32m IntervalListTools (Picard) [36mA tool for performing various IntervalList manipulations[0m
[32m LiftOverIntervalList (Picard) [36mLifts over an interval list from one reference build to another. [0m
[32m PreprocessIntervals [36mPrepares bins for coverage collection[0m
[32m SplitIntervals [36mSplit intervals into sub-interval files.[0m
[37m--------------------------------------------------------------------------------------
[0m[31mMetagenomics: Tools that perform metagenomic analysis, e.g. microbial community composition and pathogen detection[0m
[32m PathSeqBuildKmers [36mBuilds set of host reference k-mers[0m
[32m PathSeqBuildReferenceTaxonomy [36mBuilds a taxonomy datafile of the microbe reference[0m
[32m PathSeqBwaSpark [36mStep 2: Aligns reads to the microbe reference[0m
[32m PathSeqFilterSpark [36mStep 1: Filters low quality, low complexity, duplicate, and host reads[0m
[32m PathSeqPipelineSpark [36mCombined tool that performs all steps: read filtering, microbe reference alignment, and abundance scoring[0m
[32m PathSeqScoreSpark [36mStep 3: Classifies pathogen-aligned reads and generates abundance scores[0m
[37m--------------------------------------------------------------------------------------
[0m[31mMethylation-Specific Tools: Tools that perform methylation calling, processing bisulfite sequenced, methylation-aware aligned BAM[0m
[32m MethylationTypeCaller [31m(EXPERIMENTAL Tool) [36mIdentify methylated bases from bisulfite sequenced, methylation-aware BAMs[0m
[37m--------------------------------------------------------------------------------------
[0m[31mOther: Miscellaneous tools, e.g. those that aid in data streaming[0m
[32m CreateHadoopBamSplittingIndex [31m(BETA Tool) [36mCreate a Hadoop BAM splitting index[0m
[32m FifoBuffer (Picard) [36mProvides a large, FIFO buffer that can be used to buffer input and output streams between programs.[0m
[32m GatherBQSRReports [36mGathers scattered BQSR recalibration reports into a single file[0m
[32m GatherTranches [31m(BETA Tool) [36mGathers scattered VQSLOD tranches into a single file[0m
[32m IndexFeatureFile [36mCreates an index for a feature file, e.g. VCF or BED file.[0m
[32m ParallelCopyGCSDirectoryIntoHDFSSpark [31m(BETA Tool) [36mParallel copy a file or directory from Google Cloud Storage into the HDFS file system used by Spark[0m
[32m PrintBGZFBlockInformation [31m(EXPERIMENTAL Tool) [36mPrint information about the compressed blocks in a BGZF format file[0m
[32m ReadAnonymizer [31m(EXPERIMENTAL Tool) [36mReplace bases in reads with reference bases.[0m
[32m ReblockGVCF [36mCondenses homRef blocks in a single-sample GVCF[0m
[32m SortGff (Picard) [36mSorts a gff3 file, and adds flush directives[0m
[37m--------------------------------------------------------------------------------------
[0m[31mRead Data Manipulation: Tools that manipulate read data in SAM, BAM or CRAM format[0m
[32m AddCommentsToBam (Picard) [36mAdds comments to the header of a BAM file.[0m
[32m AddOATag (Picard) [36mRecord current alignment information to OA tag.[0m
[32m AddOrReplaceReadGroups (Picard) [36mAssigns all the reads in a file to a single new read-group.[0m
[32m AddOriginalAlignmentTags [31m(EXPERIMENTAL Tool) [36mAdds Original Alignment tag and original mate contig tag[0m
[32m ApplyBQSR [36mApply base quality score recalibration[0m
[32m ApplyBQSRSpark [31m(BETA Tool) [36mApply base quality score recalibration on Spark[0m
[32m BQSRPipelineSpark [31m(BETA Tool) [36mBoth steps of BQSR (BaseRecalibrator and ApplyBQSR) on Spark[0m
[32m BamToBfq (Picard) [36mConverts a BAM file into a BFQ (binary fastq formatted) file[0m
[32m BaseRecalibrator [36mGenerates recalibration table for Base Quality Score Recalibration (BQSR)[0m
[32m BaseRecalibratorSpark [31m(BETA Tool) [36mGenerate recalibration table for Base Quality Score Recalibration (BQSR) on Spark[0m
[32m BuildBamIndex (Picard) [36mGenerates a BAM index ".bai" file. [0m
[32m BwaAndMarkDuplicatesPipelineSpark [31m(BETA Tool) [36mTakes name-sorted file and runs BWA and MarkDuplicates.[0m
[32m BwaSpark [31m(BETA Tool) [36mAlign reads to a given reference using BWA on Spark[0m
[32m CleanSam (Picard) [36mCleans a SAM/BAM/CRAM files, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads[0m
[32m ClipReads [36mClip reads in a SAM/BAM/CRAM file[0m
[32m CollectDuplicateMetrics (Picard) [36mCollect Duplicate metrics from marked file.[0m
[32m ConvertHeaderlessHadoopBamShardToBam [31m(BETA Tool) [36mConvert a headerless BAM shard into a readable BAM[0m
[32m DownsampleByDuplicateSet [31m(BETA Tool) [36mDiscard a set fraction of duplicate sets from a UMI-grouped bam[0m
[32m DownsampleSam (Picard) [36mDownsample a SAM or BAM file.[0m
[32m ExtractOriginalAlignmentRecordsByNameSpark [31m(BETA Tool) [36mSubsets reads by name[0m
[32m FastqToSam (Picard) [36mConverts a FASTQ file to an unaligned BAM or SAM file[0m
[32m FilterSamReads (Picard) [36mSubsets reads from a SAM/BAM/CRAM file by applying one of several filters.[0m
[32m FixMateInformation (Picard) [36mVerify mate-pair information between mates and fix if needed.[0m
[32m FixMisencodedBaseQualityReads [36mFix Illumina base quality scores in a SAM/BAM/CRAM file[0m
[32m GatherBamFiles (Picard) [36mConcatenate efficiently BAM files that resulted from a scattered parallel analysis[0m
[32m LeftAlignIndels [36mLeft-aligns indels from reads in a SAM/BAM/CRAM file[0m
[32m MarkDuplicates (Picard) [36mIdentifies duplicate reads. [0m
[32m MarkDuplicatesSpark [36mMarkDuplicates on Spark[0m
[32m MarkDuplicatesWithMateCigar (Picard) [36mIdentifies duplicate reads, accounting for mate CIGAR. [0m
[32m MergeBamAlignment (Picard) [36mMerge alignment data from a SAM or BAM with data in an unmapped BAM file. [0m
[32m MergeSamFiles (Picard) [36mMerges multiple SAM/BAM/CRAM (and/or) files into a single file. [0m
[32m PositionBasedDownsampleSam (Picard) [36mDownsample a SAM or BAM file to retain a subset of the reads based on the reads location in each tile in the flowcell.[0m
[32m PostProcessReadsForRSEM [31m(BETA Tool) [36mReorder reads before running RSEM[0m
[32m PrintDistantMates [36mUnmaps reads with distant mates.[0m
[32m PrintReads [36mPrint reads in the SAM/BAM/CRAM file[0m
[32m PrintReadsHeader [36mPrint the header from a SAM/BAM/CRAM file[0m
[32m PrintReadsSpark [36mPrintReads on Spark[0m
[32m ReorderSam (Picard) [36mReorders reads in a SAM or BAM file to match ordering in a second reference file.[0m
[32m ReplaceSamHeader (Picard) [36mReplaces the SAMFileHeader in a SAM/BAM/CRAM file. [0m
[32m RevertBaseQualityScores [36mRevert Quality Scores in a SAM/BAM/CRAM file[0m
[32m RevertOriginalBaseQualitiesAndAddMateCigar (Picard)[36mReverts the original base qualities and adds the mate cigar tag to read-group files[0m
[32m RevertSam (Picard) [36mReverts SAM/BAM/CRAM files to a previous state. [0m
[32m RevertSamSpark [31m(BETA Tool) [36mReverts SAM, BAM or CRAM files to a previous state.[0m
[32m SamFormatConverter (Picard) [36mConvert a BAM file to a SAM file, or a SAM to a BAM[0m
[32m SamToFastq (Picard) [36mConverts a SAM/BAM/CRAM file to FASTQ.[0m
[32m SamToFastqWithTags (Picard) [36mConverts a SAM or BAM file to FASTQ alongside FASTQs created from tags.[0m
[32m SetNmAndUqTags (Picard) [36mDEPRECATED: Use SetNmMdAndUqTags instead.[0m
[32m SetNmMdAndUqTags (Picard) [36mFixes the NM, MD, and UQ tags in a SAM/BAM/CRAM file [0m
[32m SimpleMarkDuplicatesWithMateCigar (Picard) [31m(EXPERIMENTAL Tool) [36mExamines aligned records in the supplied SAM or BAM file to locate duplicate molecules.[0m
[32m SortSam (Picard) [36mSorts a SAM, BAM or CRAM file. [0m
[32m SortSamSpark [31m(BETA Tool) [36mSortSam on Spark (works on SAM/BAM/CRAM)[0m
[32m SplitNCigarReads [36mSplit Reads with N in Cigar[0m
[32m SplitReads [36mOutputs reads from a SAM/BAM/CRAM by read group, sample and library name[0m
[32m SplitSamByLibrary (Picard) [36mSplits a SAM/BAM/CRAM file into individual files by library[0m
[32m SplitSamByNumberOfReads (Picard) [36mSplits a SAM/BAM/CRAM file to multiple files.[0m
[32m TransferReadTags [31m(EXPERIMENTAL Tool) [36mIncorporate read tags in a SAM file to that of a matching SAM file[0m
[32m UmiAwareMarkDuplicatesWithMateCigar (Picard) [31m(EXPERIMENTAL Tool) [36mIdentifies duplicate reads using information from read positions and UMIs. [0m
[32m UnmarkDuplicates [36mClears the 0x400 duplicate SAM flag[0m
[37m--------------------------------------------------------------------------------------
[0m[31mReference: Tools that analyze and manipulate FASTA format references[0m
[32m BaitDesigner (Picard) [36mDesigns oligonucleotide baits for hybrid selection reactions.[0m
[32m BwaMemIndexImageCreator [36mCreate a BWA-MEM index image file for use with GATK BWA tools[0m
[32m CheckReferenceCompatibility [31m(EXPERIMENTAL Tool) [36mCheck a BAM/VCF for compatibility against specified references.[0m
[32m CompareReferences [31m(EXPERIMENTAL Tool) [36mDisplay reference comparison as a tab-delimited table and summarize reference differences.[0m
[32m ComposeSTRTableFile [36mComposes a genome-wide STR location table used for DragSTR model auto-calibration[0m
[32m CountBasesInReference [36mCount the numbers of each base in a reference file[0m
[32m CreateSequenceDictionary (Picard) [36mCreates a sequence dictionary for a reference sequence. [0m
[32m ExtractSequences (Picard) [36mSubsets intervals from a reference sequence to a new FASTA file.[0m
[32m FastaAlternateReferenceMaker [36mCreate an alternative reference by combining a fasta with a vcf.[0m
[32m FastaReferenceMaker [36mCreate snippets of a fasta file[0m
[32m FindBadGenomicKmersSpark [31m(BETA Tool) [36mIdentifies sequences that occur at high frequency in a reference[0m
[32m NonNFastaSize (Picard) [36mCounts the number of non-N bases in a fasta file.[0m
[32m NormalizeFasta (Picard) [36mNormalizes lines of sequence in a FASTA file to be of the same length.[0m
[32m ScatterIntervalsByNs (Picard) [36mWrites an interval list created by splitting a reference at Ns.[0m
[32m ShiftFasta [31m(BETA Tool) [36mCreates a shifted fasta file and shift_back file[0m
[37m--------------------------------------------------------------------------------------
[0m[31mShort Variant Discovery: Tools that perform variant calling and genotyping for short variants (SNPs, SNVs and Indels)[0m
[32m CalibrateDragstrModel [36mestimates the parameters for the DRAGstr model[0m
[32m CombineGVCFs [36mMerges one or more HaplotypeCaller GVCF files into a single GVCF with appropriate annotations[0m
[32m GenomicsDBImport [36mImport VCFs to GenomicsDB[0m
[32m GenotypeGVCFs [36mPerform joint genotyping on one or more samples pre-called with HaplotypeCaller[0m
[32m GnarlyGenotyper [31m(BETA Tool) [36mPerform "quick and dirty" joint genotyping on one or more samples pre-called with HaplotypeCaller[0m
[32m HaplotypeBasedVariantRecaller [31m(EXPERIMENTAL Tool) [36mCalculate likelihood matrix for each Allele in VCF against a set of Reads limited by a set of Haplotypes[0m
[32m HaplotypeCaller [36mCall germline SNPs and indels via local re-assembly of haplotypes[0m
[32m HaplotypeCallerSpark [31m(BETA Tool) [36mHaplotypeCaller on Spark[0m
[32m LearnReadOrientationModel [36mGet the maximum likelihood estimates of artifact prior probabilities in the orientation bias mixture model filter[0m
[32m MergeMutectStats [36mMerge the stats output by scatters of a single Mutect2 job[0m
[32m Mutect2 [36mCall somatic SNVs and indels via local assembly of haplotypes[0m
[32m RampedHaplotypeCaller [31m(EXPERIMENTAL Tool) [36mCall germline SNPs and indels via local re-assembly of haplotypes (ramped version)[0m
[32m ReadsPipelineSpark [31m(BETA Tool) [36mRuns BWA (if specified), MarkDuplicates, BQSR, and HaplotypeCaller on unaligned or aligned reads to generate a VCF.[0m
[37m--------------------------------------------------------------------------------------
[0m[31mStructural Variant Discovery: Tools that detect structural variants [0m
[32m CollectSVEvidence [31m(BETA Tool) [36mGathers paired-end and split read evidence files for use in the GATK-SV pipeline.[0m
[32m CondenseDepthEvidence [31m(EXPERIMENTAL Tool) [36mMerges adjacent DepthEvidence records.[0m
[32m CpxVariantReInterpreterSpark [31m(BETA Tool) [36m(Internal) Tries to extract simple variants from a provided GATK-SV CPX.vcf[0m
[32m DiscoverVariantsFromContigAlignmentsSAMSpark [31m(BETA Tool) [36m(Internal) Examines aligned contigs from local assemblies and calls structural variants[0m
[32m ExtractSVEvidenceSpark [31m(BETA Tool) [36m(Internal) Extracts evidence of structural variations from reads[0m
[32m FindBreakpointEvidenceSpark [31m(BETA Tool) [36m(Internal) Produces local assemblies of genomic regions that may harbor structural variants[0m
[32m JointGermlineCNVSegmentation [31m(BETA Tool) [36mCombine segmented gCNV VCFs.[0m
[32m PrintReadCounts [31m(EXPERIMENTAL Tool) [36mPrints count files for CNV determination.[0m
[32m PrintSVEvidence [31m(EXPERIMENTAL Tool) [36mMerges SV evidence records.[0m
[32m SVAnnotate [36mAdds gene overlap and variant consequence annotations to SV VCF from GATK-SV pipeline[0m
[32m SVCluster [31m(BETA Tool) [36mClusters structural variants[0m
[32m SiteDepthtoBAF [31m(EXPERIMENTAL Tool) [36mConvert SiteDepth to BafEvidence[0m
[32m StructuralVariantDiscoverer [31m(BETA Tool) [36m(Internal) Examines aligned contigs from local assemblies and calls structural variants or their breakpoints[0m
[32m StructuralVariationDiscoveryPipelineSpark [31m(BETA Tool) [36mRuns the structural variation discovery workflow on a single sample[0m
[32m SvDiscoverFromLocalAssemblyContigAlignmentsSpark [31m(BETA Tool) [36m(Internal) Examines aligned contigs from local assemblies and calls structural variants or their breakpoints[0m
[37m--------------------------------------------------------------------------------------
[0m[31mVariant Evaluation and Refinement: Tools that evaluate and refine variant calls, e.g. with annotations not offered by the engine[0m
[32m AlleleFrequencyQC [31m(BETA Tool) [36mGeneral-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more)[0m
[32m AnnotateVcfWithBamDepth [36m(Internal) Annotate a vcf with a bam's read depth at each variant locus[0m
[32m AnnotateVcfWithExpectedAlleleFraction [36m(Internal) Annotate a vcf with expected allele fractions in pooled sequencing[0m
[32m CalculateGenotypePosteriors [36mCalculate genotype posterior probabilities given family and/or known population genotypes[0m
[32m CalculateMixingFractions [36m(Internal) Calculate proportions of different samples in a pooled bam[0m
[32m Concordance [36mEvaluate concordance of an input VCF against a validated truth VCF[0m
[32m CountFalsePositives [31m(BETA Tool) [36mCount PASS variants[0m
[32m CountVariants [36mCounts variant records in a VCF file, regardless of filter status.[0m
[32m CountVariantsSpark [36mCountVariants on Spark[0m
[32m EvaluateInfoFieldConcordance [31m(BETA Tool) [36mEvaluate concordance of info fields in an input VCF against a validated truth VCF[0m
[32m FilterFuncotations [31m(EXPERIMENTAL Tool) [36mFilter variants based on clinically-significant Funcotations.[0m
[32m FindMendelianViolations (Picard) [36mFinds mendelian violations of all types within a VCF[0m
[32m FuncotateSegments [31m(BETA Tool) [36mFunctional annotation for segment files. The output formats are not well-defined and subject to change.[0m
[32m Funcotator [36mFunctional Annotator[0m
[32m FuncotatorDataSourceDownloader [36mData source downloader for Funcotator.[0m
[32m GenotypeConcordance (Picard) [36mCalculates the concordance between genotype data of one sample in each of two VCFs - truth (or reference) vs. calls.[0m
[32m MergeMutect2CallsWithMC3 [31m(EXPERIMENTAL Tool) [36mUNSUPPORTED. FOR EVALUATION ONLY. Merge M2 calls with MC[0m
[32m ReferenceBlockConcordance [36mEvaluate GVCF reference block concordance of an input GVCF against a truth GVCF[0m
[32m ValidateBasicSomaticShortMutations [31m(EXPERIMENTAL Tool) [36mCheck variants against tumor-normal bams representing the same samples, though not the ones from the actual calls.[0m
[32m ValidateVariants [36mValidate VCF[0m
[32m VariantEval [31m(BETA Tool) [36mGeneral-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more)[0m
[32m VariantsToTable [36mExtract fields from a VCF file to a tab-delimited table[0m
[37m--------------------------------------------------------------------------------------
[0m[31mVariant Filtering: Tools that filter variants by annotating the FILTER column[0m
[32m ApplyVQSR [36m Apply a score cutoff to filter variants based on a recalibration table[0m
[32m CNNScoreVariants [36mApply a Convolutional Neural Net to filter annotated variants[0m
[32m CNNVariantTrain [31m(EXPERIMENTAL Tool) [36mTrain a CNN model for filtering variants[0m
[32m CNNVariantWriteTensors [31m(EXPERIMENTAL Tool) [36mWrite variant tensors for training a CNN to filter variants[0m
[32m CreateSomaticPanelOfNormals [31m(BETA Tool) [36mMake a panel of normals for use with Mutect2[0m
[32m ExtractVariantAnnotations [31m(BETA Tool) [36mExtracts site-level variant annotations, labels, and other metadata from a VCF file to HDF5 files[0m
[32m FilterAlignmentArtifacts [31m(EXPERIMENTAL Tool) [36mFilter alignment artifacts from a vcf callset.[0m
[32m FilterMutectCalls [36mFilter somatic SNVs and indels called by Mutect2[0m
[32m FilterVariantTranches [36mApply tranche filtering[0m
[32m FilterVcf (Picard) [36mHard filters a VCF.[0m
[32m MTLowHeteroplasmyFilterTool [36mIf too many low het sites, filter all low het sites[0m
[32m NuMTFilterTool [36mUses the median autosomal coverage and the allele depth to determine whether the allele might be a NuMT[0m
[32m ScoreVariantAnnotations [31m(BETA Tool) [36mScores variant calls in a VCF file based on site-level annotations using a previously trained model[0m
[32m TrainVariantAnnotationsModel [31m(BETA Tool) [36mTrains a model for scoring variant calls based on site-level annotations[0m
[32m VariantFiltration [36mFilter variant calls based on INFO and/or FORMAT annotations[0m
[32m VariantRecalibrator [36mBuild a recalibration model to score variant quality for filtering purposes[0m
[37m--------------------------------------------------------------------------------------
[0m[31mVariant Manipulation: Tools that manipulate variant call format (VCF) data[0m
[32m FixVcfHeader (Picard) [36mReplaces or fixes a VCF header.[0m
[32m GatherVcfs (Picard) [36mGathers multiple VCF files from a scatter operation into a single VCF file[0m
[32m GatherVcfsCloud [31m(BETA Tool) [36mGathers multiple VCF files from a scatter operation into a single VCF file[0m
[32m LeftAlignAndTrimVariants [36mLeft align and trim vairants[0m
[32m LiftoverVcf (Picard) [36mLifts over a VCF file from one reference build to another. [0m
[32m MakeSitesOnlyVcf (Picard) [36mCreates a VCF that contains all the site-level information for all records in the input VCF but no genotype information.[0m
[32m MakeVcfSampleNameMap (Picard) [36mCreates a TSV from sample name to VCF/GVCF path, with one line per input.[0m
[32m MergeVcfs (Picard) [36mCombines multiple variant files into a single variant file[0m
[32m PrintVariantsSpark [36mPrints out variants from the input VCF.[0m
[32m RemoveNearbyIndels [36m(Internal) Remove indels from the VCF file that are close to each other.[0m
[32m RenameSampleInVcf (Picard) [36mRenames a sample within a VCF or BCF.[0m
[32m SelectVariants [36mSelect a subset of variants from a VCF file[0m
[32m SortVcf (Picard) [36mSorts one or more VCF files. [0m
[32m SplitVcfs (Picard) [36mSplits SNPs and INDELs into separate files. [0m
[32m UpdateVCFSequenceDictionary [36mUpdates the sequence dictionary in a variant file.[0m
[32m UpdateVcfSequenceDictionary (Picard) [36mTakes a VCF and a second file that contains a sequence dictionary and updates the VCF with the new sequence dictionary.[0m
[32m VariantAnnotator [36mTool for adding annotations to VCF files[0m
[32m VcfFormatConverter (Picard) [36mConverts VCF to BCF or BCF to VCF. [0m
[32m VcfToIntervalList (Picard) [36mConverts a VCF or BCF file to a Picard Interval List[0m
[37m--------------------------------------------------------------------------------------
[0m
***********************************************************************
A USER ERROR has occurred: '-Xmx104857M' is not a valid command.
***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
Using GATK jar /gatk/gatk-package-4.3.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /gatk/gatk-package-4.3.0.0-local.jar -Xmx104857M SplitNCigarReads -R input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta -I output.temp/Le1-13-502-701_1.fastq.gz_addrg_repN.bam -O output2/Le1-13-502-701_1.fastq.gz.bam
/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
INFO 2023-02-28 23:40:56 AddOrReplaceReadGroups
********** NOTE: Picard's command line syntax is changing.
**********
********** For more information, please see:
********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
**********
********** The command line looks like this in the new syntax:
**********
********** AddOrReplaceReadGroups -I output/Le1-17-502-703_1.fastq.gz.bam -O output.temp/Le1-17-502-703_1.fastq.gz_addrg.bam -SO coordinate -RGID Le1-17-502-703_1.fastq.gz -RGLB library -RGPL Illumina -RGPU Illumina -RGSM Le1-17-502-703_1.fastq.gz
**********
23:40:57.347 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/picard-2.18.27-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Tue Feb 28 23:40:57 GMT 2023] AddOrReplaceReadGroups INPUT=output/Le1-17-502-703_1.fastq.gz.bam OUTPUT=output.temp/Le1-17-502-703_1.fastq.gz_addrg.bam SORT_ORDER=coordinate RGID=Le1-17-502-703_1.fastq.gz RGLB=library RGPL=Illumina RGPU=Illumina RGSM=Le1-17-502-703_1.fastq.gz VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Tue Feb 28 23:40:57 GMT 2023] Executing as ?@4855180c684a on Linux 3.10.0-1160.36.2.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.27-SNAPSHOT
INFO 2023-02-28 23:40:57 AddOrReplaceReadGroups Created read-group ID=Le1-17-502-703_1.fastq.gz PL=Illumina LB=library SM=Le1-17-502-703_1.fastq.gz
[Tue Feb 28 23:41:10 GMT 2023] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 0.22 minutes.
Runtime.totalMemory()=2583691264
[1m[31mUSAGE: [32m[1m[31m [-h]
[0m[1m[31mAvailable Programs:
[0m[37m--------------------------------------------------------------------------------------
[0m[31mBase Calling: Tools that process sequencing machine data, e.g. Illumina base calls, and detect sequencing level attributes, e.g. adapters[0m
[32m CheckIlluminaDirectory (Picard) [36mAsserts the validity for specified Illumina basecalling data. [0m
[32m CollectIlluminaBasecallingMetrics (Picard) [36mCollects Illumina Basecalling metrics for a sequencing run. [0m
[32m CollectIlluminaLaneMetrics (Picard) [36mCollects Illumina lane metrics for the given BaseCalling analysis directory.[0m
[32m ExtractIlluminaBarcodes (Picard) [36mTool determines the barcode for each read in an Illumina lane. [0m
[32m IlluminaBasecallsToFastq (Picard) [36mGenerate FASTQ file(s) from Illumina basecall read data. [0m
[32m IlluminaBasecallsToSam (Picard) [36mTransforms raw Illumina sequencing data into an unmapped SAM, BAM or CRAM file.[0m
[32m MarkIlluminaAdapters (Picard) [36mReads a SAM/BAM/CRAM file and rewrites it with new adapter-trimming tags. [0m
[37m--------------------------------------------------------------------------------------
[0m[31mCopy Number Variant Discovery: Tools that analyze read coverage to detect copy number variants.[0m
[32m AnnotateIntervals [36mAnnotates intervals with GC content, mappability, and segmental-duplication content[0m
[32m CallCopyRatioSegments [36mCalls copy-ratio segments as amplified, deleted, or copy-number neutral[0m
[32m CombineSegmentBreakpoints [31m(EXPERIMENTAL Tool) [36mCombine the breakpoints of two segment files and annotate the resulting intervals with chosen columns from each file.[0m
[32m CreateReadCountPanelOfNormals [36mCreates a panel of normals for read-count denoising[0m
[32m DenoiseReadCounts [36mDenoises read counts to produce denoised copy ratios[0m
[32m DetermineGermlineContigPloidy [36mDetermines the baseline contig ploidy for germline samples given counts data[0m
[32m FilterIntervals [36mFilters intervals based on annotations and/or count statistics[0m
[32m GermlineCNVCaller [36mCalls copy-number variants in germline samples given their counts and the output of DetermineGermlineContigPloidy[0m
[32m MergeAnnotatedRegions [31m(EXPERIMENTAL Tool) [36mMerge annotated genomic regions based entirely on touching/overlapping intervals.[0m
[32m MergeAnnotatedRegionsByAnnotation [31m(EXPERIMENTAL Tool) [36mMerge annotated genomic regions within specified distance if annotation value(s) are exactly the same.[0m
[32m ModelSegments [36mModels segmented copy ratios from denoised copy ratios and segmented minor-allele fractions from allelic counts[0m
[32m PlotDenoisedCopyRatios [36mCreates plots of denoised copy ratios[0m
[32m PlotModeledSegments [36mCreates plots of denoised and segmented copy-ratio and minor-allele-fraction estimates[0m
[32m PostprocessGermlineCNVCalls [36mPostprocesses the output of GermlineCNVCaller and generates VCFs and denoised copy ratios[0m
[32m TagGermlineEvents [31m(EXPERIMENTAL Tool) [36mDo a simplistic tagging of germline events in a tumor segment file.[0m
[37m--------------------------------------------------------------------------------------
[0m[31mCoverage Analysis: Tools that count coverage, e.g. depth per allele[0m
[32m ASEReadCounter [36mGenerates table of filtered base counts at het sites for allele specific expression[0m
[32m AnalyzeSaturationMutagenesis [31m(BETA Tool) [36m(EXPERIMENTAL) Processes reads from a MITESeq or other saturation mutagenesis experiment.[0m
[32m CollectAllelicCounts [36mCollects reference and alternate allele counts at specified sites[0m
[32m CollectAllelicCountsSpark [36mCollects reference and alternate allele counts at specified sites[0m
[32m CollectF1R2Counts [36mCollect F1R2 read counts for the Mutect2 orientation bias mixture model filter[0m
[32m CollectReadCounts [36mCollects read counts at specified intervals[0m
[32m CountBases [36mCount bases in a SAM/BAM/CRAM file[0m
[32m CountBasesSpark [36mCounts bases in the input SAM/BAM[0m
[32m CountReads [36mCount reads in a SAM/BAM/CRAM file[0m
[32m CountReadsSpark [36mCounts reads in the input SAM/BAM[0m
[32m DepthOfCoverage [31m(BETA Tool) [36mGenerate coverage summary information for reads data[0m
[32m GatherNormalArtifactData [36mCombine output files from GetNormalArtifactData in the order defined by a sequence dictionary[0m
[32m GeneExpressionEvaluation [31m(BETA Tool) [36mEvaluate gene expression from RNA-seq reads aligned to genome.[0m
[32m GetNormalArtifactData [36mCollects data for training normal artifact filter[0m
[32m GetPileupSummaries [36mTabulates pileup metrics for inferring contamination[0m
[32m LocalAssembler [31m(BETA Tool) [36mLocal assembler for SVs[0m
[32m Pileup [36mPrints read alignments in samtools pileup format[0m
[32m PileupSpark [31m(BETA Tool) [36mPrints read alignments in samtools pileup format[0m
[37m--------------------------------------------------------------------------------------
[0m[31mDiagnostics and Quality Control: Tools that collect sequencing quality related and comparative metrics[0m
[32m AccumulateQualityYieldMetrics (Picard) [36mCombines multiple QualityYieldMetrics files into a single file.[0m
[32m AccumulateVariantCallingMetrics (Picard) [36mCombines multiple Variant Calling Metrics files into a single file[0m
[32m AnalyzeCovariates [36mEvaluate and compare base quality score recalibration (BQSR) tables[0m
[32m BamIndexStats (Picard) [36mGenerate index statistics from a BAM file[0m
[32m CalcMetadataSpark [31m(BETA Tool) [36m(Internal) Collects read metrics relevant to structural variant discovery[0m
[32m CalculateContamination [36mCalculate the fraction of reads coming from cross-sample contamination[0m
[32m CalculateFingerprintMetrics (Picard) [36mCalculate statistics on fingerprints, checking their viability[0m
[32m CalculateReadGroupChecksum (Picard) [36mCreates a hash code based on the read groups (RG). [0m
[32m CheckDuplicateMarking (Picard) [36mChecks the consistency of duplicate markings.[0m
[32m CheckFingerprint (Picard) [36mComputes a fingerprint from the supplied input (SAM/BAM/CRAM or VCF) file and compares it to the provided genotypes[0m
[32m CheckPileup [36mCompare GATK's internal pileup to a reference Samtools mpileup[0m
[32m CheckTerminatorBlock (Picard) [36mAsserts the provided gzip file's (e.g., BAM) last block is well-formed; RC 100 otherwise[0m
[32m ClusterCrosscheckMetrics (Picard) [36mClusters the results of a CrosscheckFingerprints run by LOD score[0m
[32m CollectAlignmentSummaryMetrics (Picard) [36mProduces a summary of alignment metrics from a SAM or BAM file. [0m
[32m CollectArraysVariantCallingMetrics (Picard) [36mCollects summary and per-sample from the provided arrays VCF file[0m
[32m CollectBaseDistributionByCycle (Picard) [36mChart the nucleotide distribution per cycle in a SAM or BAM file[0m
[32m CollectBaseDistributionByCycleSpark [31m(BETA Tool) [36mCollects base distribution per cycle in SAM/BAM/CRAM file(s).[0m
[32m CollectGcBiasMetrics (Picard) [36mCollect metrics regarding GC bias. [0m
[32m CollectHiSeqXPfFailMetrics (Picard) [36mClassify PF-Failing reads in a HiSeqX Illumina Basecalling directory into various categories.[0m
[32m CollectHsMetrics (Picard) [36mCollects hybrid-selection (HS) metrics for a SAM or BAM file. [0m
[32m CollectIndependentReplicateMetrics (Picard) [31m(EXPERIMENTAL Tool) [36mEstimates the rate of independent replication rate of reads within a bam.
[0m
[32m CollectInsertSizeMetrics (Picard) [36mCollect metrics about the insert size distribution of a paired-end library. [0m
[32m CollectInsertSizeMetricsSpark [31m(BETA Tool) [36mCollects insert size distribution information on alignment data[0m
[32m CollectJumpingLibraryMetrics (Picard) [36mCollect jumping library metrics. [0m
[32m CollectMultipleMetrics (Picard) [36mCollect multiple classes of metrics. [0m
[32m CollectMultipleMetricsSpark [31m(BETA Tool) [36mRuns multiple metrics collection modules for a given alignment file[0m
[32m CollectOxoGMetrics (Picard) [36mCollect metrics to assess oxidative artifacts.[0m
[32m CollectQualityYieldMetrics (Picard) [36mCollect metrics about reads that pass quality thresholds and Illumina-specific filters. [0m
[32m CollectQualityYieldMetricsSpark [31m(BETA Tool) [36mCollects quality yield metrics from SAM/BAM/CRAM file(s).[0m
[32m CollectRawWgsMetrics (Picard) [36mCollect whole genome sequencing-related metrics. [0m
[32m CollectRnaSeqMetrics (Picard) [36mProduces RNA alignment metrics for a SAM or BAM file. [0m
[32m CollectRrbsMetrics (Picard) [36mCollects metrics from reduced representation bisulfite sequencing (Rrbs) data. [0m
[32m CollectSamErrorMetrics (Picard) [36mProgram to collect error metrics on bases stratified in various ways.[0m
[32m CollectSequencingArtifactMetrics (Picard) [36mCollect metrics to quantify single-base sequencing artifacts. [0m
[32m CollectTargetedPcrMetrics (Picard) [36mCalculate PCR-related metrics from targeted sequencing data. [0m
[32m CollectVariantCallingMetrics (Picard) [36mCollects per-sample and aggregate (spanning all samples) metrics from the provided VCF file[0m
[32m CollectWgsMetrics (Picard) [36mCollect metrics about coverage and performance of whole genome sequencing (WGS) experiments.[0m
[32m CollectWgsMetricsWithNonZeroCoverage (Picard)[31m(EXPERIMENTAL Tool) [36mCollect metrics about coverage and performance of whole genome sequencing (WGS) experiments. [0m
[32m CompareBaseQualities [36mCompares the base qualities of two SAM/BAM/CRAM files[0m
[32m CompareDuplicatesSpark [31m(BETA Tool) [36mDetermine if two potentially identical BAMs have the same duplicate reads[0m
[32m CompareMetrics (Picard) [36mCompare two metrics files.[0m
[32m CompareSAMs (Picard) [36mCompare two input SAM/BAM/CRAM files. [0m
[32m ConvertHaplotypeDatabaseToVcf (Picard) [36mConvert Haplotype database file to vcf[0m
[32m ConvertSequencingArtifactToOxoG (Picard) [36mExtract OxoG metrics from generalized artifacts metrics. [0m
[32m CrosscheckFingerprints (Picard) [36mChecks that all data in the input files appear to have come from the same individual[0m
[32m CrosscheckReadGroupFingerprints (Picard) [36mDEPRECATED: USE CrosscheckFingerprints. [0m
[32m DumpTabixIndex [36mDumps a tabix index file.[0m
[32m EstimateLibraryComplexity (Picard) [36mEstimates the numbers of unique molecules in a sequencing library. [0m
[32m ExtractFingerprint (Picard) [36mComputes a fingerprint from the input file.[0m
[32m FlagStat [36mAccumulate flag statistics given a BAM file[0m
[32m FlagStatSpark [36mSpark tool to accumulate flag statistics[0m
[32m GatherPileupSummaries [36mCombine output files from GetPileupSummary in the order defined by a sequence dictionary[0m
[32m GetSampleName [36mEmit a single sample name[0m
[32m IdentifyContaminant (Picard) [36mComputes a fingerprint from the supplied SAM/BAM file, given a contamination estimate.[0m
[32m LiftOverHaplotypeMap (Picard) [36mLifts over a haplotype database from one reference to another[0m
[32m MeanQualityByCycle (Picard) [36mCollect mean quality by cycle.[0m
[32m MeanQualityByCycleSpark [31m(BETA Tool) [36mMeanQualityByCycle on Spark[0m
[32m QualityScoreDistribution (Picard) [36mChart the distribution of quality scores. [0m
[32m QualityScoreDistributionSpark [31m(BETA Tool) [36mQualityScoreDistribution on Spark[0m
[32m ValidateSamFile (Picard) [36mValidates a SAM/BAM/CRAM file.[0m
[32m ViewSam (Picard) [36mPrints a SAM or BAM file to the screen[0m
[37m--------------------------------------------------------------------------------------
[0m[31mExample Tools: Example tools that show developers how to implement new tools[0m
[32m ExampleMultiFeatureWalker [36mExample of a MultiFeatureWalker subclass.[0m
[32m HtsgetReader [31m(EXPERIMENTAL Tool) [36mDownload a file using htsget[0m
[37m--------------------------------------------------------------------------------------
[0m[31mFlow Based Tools: Tools designed specifically to operate on flow based data[0m
[32m CalculateAverageCombinedAnnotations [31m(EXPERIMENTAL Tool) [36mDivides annotations that were summed by genomicsDB by number of samples to calculate average.[0m
[32m FlowFeatureMapper [31m(EXPERIMENTAL Tool) [36mMap/find features in BAM file, output VCF. Initially mapping SNVs[0m
[32m GroundTruthReadsBuilder [31m(EXPERIMENTAL Tool) [36mProduces a flexible and robust ground truth set for base calling training[0m
[32m SplitCRAM [31m(EXPERIMENTAL Tool) [36mSplit CRAM files to smaller files efficiently[0m
[37m--------------------------------------------------------------------------------------
[0m[31mGenotyping Arrays Manipulation: Tools that manipulate data generated by Genotyping arrays[0m
[32m BpmToNormalizationManifestCsv (Picard) [36mProgram to convert an Illumina bpm file into a bpm.csv file.[0m
[32m CombineGenotypingArrayVcfs (Picard) [36mProgram to combine multiple genotyping array VCF files into one VCF.[0m
[32m CompareGtcFiles (Picard) [36mCompares two GTC files.[0m
[32m CreateBafRegressMetricsFile (Picard) [36mProgram to generate a picard metrics file from the output of the bafRegress tool.[0m
[32m CreateExtendedIlluminaManifest (Picard) [36mCreate an Extended Illumina Manifest for usage by the Picard tool GtcToVcf[0m
[32m CreateVerifyIDIntensityContaminationMetricsFile (Picard) [36mProgram to generate a picard metrics file from the output of the VerifyIDIntensity tool.[0m
[32m GtcToVcf (Picard) [36mProgram to convert an Illumina GTC file to a VCF[0m
[32m MergePedIntoVcf (Picard) [36mProgram to merge a single-sample ped file from zCall into a single-sample VCF.[0m
[32m VcfToAdpc (Picard) [36mProgram to convert an Arrays VCF to an ADPC file.[0m
[37m--------------------------------------------------------------------------------------
[0m[31mIntervals Manipulation: Tools that process genomic intervals in various formats[0m
[32m BedToIntervalList (Picard) [36mConverts a BED file to a Picard Interval List. [0m
[32m CompareIntervalLists [36mCompare two interval lists for equality[0m
[32m IntervalListToBed (Picard) [36mConverts an Picard IntervalList file to a BED file.[0m
[32m IntervalListTools (Picard) [36mA tool for performing various IntervalList manipulations[0m
[32m LiftOverIntervalList (Picard) [36mLifts over an interval list from one reference build to another. [0m
[32m PreprocessIntervals [36mPrepares bins for coverage collection[0m
[32m SplitIntervals [36mSplit intervals into sub-interval files.[0m
[37m--------------------------------------------------------------------------------------
[0m[31mMetagenomics: Tools that perform metagenomic analysis, e.g. microbial community composition and pathogen detection[0m
[32m PathSeqBuildKmers [36mBuilds set of host reference k-mers[0m
[32m PathSeqBuildReferenceTaxonomy [36mBuilds a taxonomy datafile of the microbe reference[0m
[32m PathSeqBwaSpark [36mStep 2: Aligns reads to the microbe reference[0m
[32m PathSeqFilterSpark [36mStep 1: Filters low quality, low complexity, duplicate, and host reads[0m
[32m PathSeqPipelineSpark [36mCombined tool that performs all steps: read filtering, microbe reference alignment, and abundance scoring[0m
[32m PathSeqScoreSpark [36mStep 3: Classifies pathogen-aligned reads and generates abundance scores[0m
[37m--------------------------------------------------------------------------------------
[0m[31mMethylation-Specific Tools: Tools that perform methylation calling, processing bisulfite sequenced, methylation-aware aligned BAM[0m
[32m MethylationTypeCaller [31m(EXPERIMENTAL Tool) [36mIdentify methylated bases from bisulfite sequenced, methylation-aware BAMs[0m
[37m--------------------------------------------------------------------------------------
[0m[31mOther: Miscellaneous tools, e.g. those that aid in data streaming[0m
[32m CreateHadoopBamSplittingIndex [31m(BETA Tool) [36mCreate a Hadoop BAM splitting index[0m
[32m FifoBuffer (Picard) [36mProvides a large, FIFO buffer that can be used to buffer input and output streams between programs.[0m
[32m GatherBQSRReports [36mGathers scattered BQSR recalibration reports into a single file[0m
[32m GatherTranches [31m(BETA Tool) [36mGathers scattered VQSLOD tranches into a single file[0m
[32m IndexFeatureFile [36mCreates an index for a feature file, e.g. VCF or BED file.[0m
[32m ParallelCopyGCSDirectoryIntoHDFSSpark [31m(BETA Tool) [36mParallel copy a file or directory from Google Cloud Storage into the HDFS file system used by Spark[0m
[32m PrintBGZFBlockInformation [31m(EXPERIMENTAL Tool) [36mPrint information about the compressed blocks in a BGZF format file[0m
[32m ReadAnonymizer [31m(EXPERIMENTAL Tool) [36mReplace bases in reads with reference bases.[0m
[32m ReblockGVCF [36mCondenses homRef blocks in a single-sample GVCF[0m
[32m SortGff (Picard) [36mSorts a gff3 file, and adds flush directives[0m
[37m--------------------------------------------------------------------------------------
[0m[31mRead Data Manipulation: Tools that manipulate read data in SAM, BAM or CRAM format[0m
[32m AddCommentsToBam (Picard) [36mAdds comments to the header of a BAM file.[0m
[32m AddOATag (Picard) [36mRecord current alignment information to OA tag.[0m
[32m AddOrReplaceReadGroups (Picard) [36mAssigns all the reads in a file to a single new read-group.[0m
[32m AddOriginalAlignmentTags [31m(EXPERIMENTAL Tool) [36mAdds Original Alignment tag and original mate contig tag[0m
[32m ApplyBQSR [36mApply base quality score recalibration[0m
[32m ApplyBQSRSpark [31m(BETA Tool) [36mApply base quality score recalibration on Spark[0m
[32m BQSRPipelineSpark [31m(BETA Tool) [36mBoth steps of BQSR (BaseRecalibrator and ApplyBQSR) on Spark[0m
[32m BamToBfq (Picard) [36mConverts a BAM file into a BFQ (binary fastq formatted) file[0m
[32m BaseRecalibrator [36mGenerates recalibration table for Base Quality Score Recalibration (BQSR)[0m
[32m BaseRecalibratorSpark [31m(BETA Tool) [36mGenerate recalibration table for Base Quality Score Recalibration (BQSR) on Spark[0m
[32m BuildBamIndex (Picard) [36mGenerates a BAM index ".bai" file. [0m
[32m BwaAndMarkDuplicatesPipelineSpark [31m(BETA Tool) [36mTakes name-sorted file and runs BWA and MarkDuplicates.[0m
[32m BwaSpark [31m(BETA Tool) [36mAlign reads to a given reference using BWA on Spark[0m
[32m CleanSam (Picard) [36mCleans a SAM/BAM/CRAM files, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads[0m
[32m ClipReads [36mClip reads in a SAM/BAM/CRAM file[0m
[32m CollectDuplicateMetrics (Picard) [36mCollect Duplicate metrics from marked file.[0m
[32m ConvertHeaderlessHadoopBamShardToBam [31m(BETA Tool) [36mConvert a headerless BAM shard into a readable BAM[0m
[32m DownsampleByDuplicateSet [31m(BETA Tool) [36mDiscard a set fraction of duplicate sets from a UMI-grouped bam[0m
[32m DownsampleSam (Picard) [36mDownsample a SAM or BAM file.[0m
[32m ExtractOriginalAlignmentRecordsByNameSpark [31m(BETA Tool) [36mSubsets reads by name[0m
[32m FastqToSam (Picard) [36mConverts a FASTQ file to an unaligned BAM or SAM file[0m
[32m FilterSamReads (Picard) [36mSubsets reads from a SAM/BAM/CRAM file by applying one of several filters.[0m
[32m FixMateInformation (Picard) [36mVerify mate-pair information between mates and fix if needed.[0m
[32m FixMisencodedBaseQualityReads [36mFix Illumina base quality scores in a SAM/BAM/CRAM file[0m
[32m GatherBamFiles (Picard) [36mConcatenate efficiently BAM files that resulted from a scattered parallel analysis[0m
[32m LeftAlignIndels [36mLeft-aligns indels from reads in a SAM/BAM/CRAM file[0m
[32m MarkDuplicates (Picard) [36mIdentifies duplicate reads. [0m
[32m MarkDuplicatesSpark [36mMarkDuplicates on Spark[0m
[32m MarkDuplicatesWithMateCigar (Picard) [36mIdentifies duplicate reads, accounting for mate CIGAR. [0m
[32m MergeBamAlignment (Picard) [36mMerge alignment data from a SAM or BAM with data in an unmapped BAM file. [0m
[32m MergeSamFiles (Picard) [36mMerges multiple SAM/BAM/CRAM (and/or) files into a single file. [0m
[32m PositionBasedDownsampleSam (Picard) [36mDownsample a SAM or BAM file to retain a subset of the reads based on the reads location in each tile in the flowcell.[0m
[32m PostProcessReadsForRSEM [31m(BETA Tool) [36mReorder reads before running RSEM[0m
[32m PrintDistantMates [36mUnmaps reads with distant mates.[0m
[32m PrintReads [36mPrint reads in the SAM/BAM/CRAM file[0m
[32m PrintReadsHeader [36mPrint the header from a SAM/BAM/CRAM file[0m
[32m PrintReadsSpark [36mPrintReads on Spark[0m
[32m ReorderSam (Picard) [36mReorders reads in a SAM or BAM file to match ordering in a second reference file.[0m
[32m ReplaceSamHeader (Picard) [36mReplaces the SAMFileHeader in a SAM/BAM/CRAM file. [0m
[32m RevertBaseQualityScores [36mRevert Quality Scores in a SAM/BAM/CRAM file[0m
[32m RevertOriginalBaseQualitiesAndAddMateCigar (Picard)[36mReverts the original base qualities and adds the mate cigar tag to read-group files[0m
[32m RevertSam (Picard) [36mReverts SAM/BAM/CRAM files to a previous state. [0m
[32m RevertSamSpark [31m(BETA Tool) [36mReverts SAM, BAM or CRAM files to a previous state.[0m
[32m SamFormatConverter (Picard) [36mConvert a BAM file to a SAM file, or a SAM to a BAM[0m
[32m SamToFastq (Picard) [36mConverts a SAM/BAM/CRAM file to FASTQ.[0m
[32m SamToFastqWithTags (Picard) [36mConverts a SAM or BAM file to FASTQ alongside FASTQs created from tags.[0m
[32m SetNmAndUqTags (Picard) [36mDEPRECATED: Use SetNmMdAndUqTags instead.[0m
[32m SetNmMdAndUqTags (Picard) [36mFixes the NM, MD, and UQ tags in a SAM/BAM/CRAM file [0m
[32m SimpleMarkDuplicatesWithMateCigar (Picard) [31m(EXPERIMENTAL Tool) [36mExamines aligned records in the supplied SAM or BAM file to locate duplicate molecules.[0m
[32m SortSam (Picard) [36mSorts a SAM, BAM or CRAM file. [0m
[32m SortSamSpark [31m(BETA Tool) [36mSortSam on Spark (works on SAM/BAM/CRAM)[0m
[32m SplitNCigarReads [36mSplit Reads with N in Cigar[0m
[32m SplitReads [36mOutputs reads from a SAM/BAM/CRAM by read group, sample and library name[0m
[32m SplitSamByLibrary (Picard) [36mSplits a SAM/BAM/CRAM file into individual files by library[0m
[32m SplitSamByNumberOfReads (Picard) [36mSplits a SAM/BAM/CRAM file to multiple files.[0m
[32m TransferReadTags [31m(EXPERIMENTAL Tool) [36mIncorporate read tags in a SAM file to that of a matching SAM file[0m
[32m UmiAwareMarkDuplicatesWithMateCigar (Picard) [31m(EXPERIMENTAL Tool) [36mIdentifies duplicate reads using information from read positions and UMIs. [0m
[32m UnmarkDuplicates [36mClears the 0x400 duplicate SAM flag[0m
[37m--------------------------------------------------------------------------------------
[0m[31mReference: Tools that analyze and manipulate FASTA format references[0m
[32m BaitDesigner (Picard) [36mDesigns oligonucleotide baits for hybrid selection reactions.[0m
[32m BwaMemIndexImageCreator [36mCreate a BWA-MEM index image file for use with GATK BWA tools[0m
[32m CheckReferenceCompatibility [31m(EXPERIMENTAL Tool) [36mCheck a BAM/VCF for compatibility against specified references.[0m
[32m CompareReferences [31m(EXPERIMENTAL Tool) [36mDisplay reference comparison as a tab-delimited table and summarize reference differences.[0m
[32m ComposeSTRTableFile [36mComposes a genome-wide STR location table used for DragSTR model auto-calibration[0m
[32m CountBasesInReference [36mCount the numbers of each base in a reference file[0m
[32m CreateSequenceDictionary (Picard) [36mCreates a sequence dictionary for a reference sequence. [0m
[32m ExtractSequences (Picard) [36mSubsets intervals from a reference sequence to a new FASTA file.[0m
[32m FastaAlternateReferenceMaker [36mCreate an alternative reference by combining a fasta with a vcf.[0m
[32m FastaReferenceMaker [36mCreate snippets of a fasta file[0m
[32m FindBadGenomicKmersSpark [31m(BETA Tool) [36mIdentifies sequences that occur at high frequency in a reference[0m
[32m NonNFastaSize (Picard) [36mCounts the number of non-N bases in a fasta file.[0m
[32m NormalizeFasta (Picard) [36mNormalizes lines of sequence in a FASTA file to be of the same length.[0m
[32m ScatterIntervalsByNs (Picard) [36mWrites an interval list created by splitting a reference at Ns.[0m
[32m ShiftFasta [31m(BETA Tool) [36mCreates a shifted fasta file and shift_back file[0m
[37m--------------------------------------------------------------------------------------
[0m[31mShort Variant Discovery: Tools that perform variant calling and genotyping for short variants (SNPs, SNVs and Indels)[0m
[32m CalibrateDragstrModel [36mestimates the parameters for the DRAGstr model[0m
[32m CombineGVCFs [36mMerges one or more HaplotypeCaller GVCF files into a single GVCF with appropriate annotations[0m
[32m GenomicsDBImport [36mImport VCFs to GenomicsDB[0m
[32m GenotypeGVCFs [36mPerform joint genotyping on one or more samples pre-called with HaplotypeCaller[0m
[32m GnarlyGenotyper [31m(BETA Tool) [36mPerform "quick and dirty" joint genotyping on one or more samples pre-called with HaplotypeCaller[0m
[32m HaplotypeBasedVariantRecaller [31m(EXPERIMENTAL Tool) [36mCalculate likelihood matrix for each Allele in VCF against a set of Reads limited by a set of Haplotypes[0m
[32m HaplotypeCaller [36mCall germline SNPs and indels via local re-assembly of haplotypes[0m
[32m HaplotypeCallerSpark [31m(BETA Tool) [36mHaplotypeCaller on Spark[0m
[32m LearnReadOrientationModel [36mGet the maximum likelihood estimates of artifact prior probabilities in the orientation bias mixture model filter[0m
[32m MergeMutectStats [36mMerge the stats output by scatters of a single Mutect2 job[0m
[32m Mutect2 [36mCall somatic SNVs and indels via local assembly of haplotypes[0m
[32m RampedHaplotypeCaller [31m(EXPERIMENTAL Tool) [36mCall germline SNPs and indels via local re-assembly of haplotypes (ramped version)[0m
[32m ReadsPipelineSpark [31m(BETA Tool) [36mRuns BWA (if specified), MarkDuplicates, BQSR, and HaplotypeCaller on unaligned or aligned reads to generate a VCF.[0m
[37m--------------------------------------------------------------------------------------
[0m[31mStructural Variant Discovery: Tools that detect structural variants [0m
[32m CollectSVEvidence [31m(BETA Tool) [36mGathers paired-end and split read evidence files for use in the GATK-SV pipeline.[0m
[32m CondenseDepthEvidence [31m(EXPERIMENTAL Tool) [36mMerges adjacent DepthEvidence records.[0m
[32m CpxVariantReInterpreterSpark [31m(BETA Tool) [36m(Internal) Tries to extract simple variants from a provided GATK-SV CPX.vcf[0m
[32m DiscoverVariantsFromContigAlignmentsSAMSpark [31m(BETA Tool) [36m(Internal) Examines aligned contigs from local assemblies and calls structural variants[0m
[32m ExtractSVEvidenceSpark [31m(BETA Tool) [36m(Internal) Extracts evidence of structural variations from reads[0m
[32m FindBreakpointEvidenceSpark [31m(BETA Tool) [36m(Internal) Produces local assemblies of genomic regions that may harbor structural variants[0m
[32m JointGermlineCNVSegmentation [31m(BETA Tool) [36mCombine segmented gCNV VCFs.[0m
[32m PrintReadCounts [31m(EXPERIMENTAL Tool) [36mPrints count files for CNV determination.[0m
[32m PrintSVEvidence [31m(EXPERIMENTAL Tool) [36mMerges SV evidence records.[0m
[32m SVAnnotate [36mAdds gene overlap and variant consequence annotations to SV VCF from GATK-SV pipeline[0m
[32m SVCluster [31m(BETA Tool) [36mClusters structural variants[0m
[32m SiteDepthtoBAF [31m(EXPERIMENTAL Tool) [36mConvert SiteDepth to BafEvidence[0m
[32m StructuralVariantDiscoverer [31m(BETA Tool) [36m(Internal) Examines aligned contigs from local assemblies and calls structural variants or their breakpoints[0m
[32m StructuralVariationDiscoveryPipelineSpark [31m(BETA Tool) [36mRuns the structural variation discovery workflow on a single sample[0m
[32m SvDiscoverFromLocalAssemblyContigAlignmentsSpark [31m(BETA Tool) [36m(Internal) Examines aligned contigs from local assemblies and calls structural variants or their breakpoints[0m
[37m--------------------------------------------------------------------------------------
[0m[31mVariant Evaluation and Refinement: Tools that evaluate and refine variant calls, e.g. with annotations not offered by the engine[0m
[32m AlleleFrequencyQC [31m(BETA Tool) [36mGeneral-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more)[0m
[32m AnnotateVcfWithBamDepth [36m(Internal) Annotate a vcf with a bam's read depth at each variant locus[0m
[32m AnnotateVcfWithExpectedAlleleFraction [36m(Internal) Annotate a vcf with expected allele fractions in pooled sequencing[0m
[32m CalculateGenotypePosteriors [36mCalculate genotype posterior probabilities given family and/or known population genotypes[0m
[32m CalculateMixingFractions [36m(Internal) Calculate proportions of different samples in a pooled bam[0m
[32m Concordance [36mEvaluate concordance of an input VCF against a validated truth VCF[0m
[32m CountFalsePositives [31m(BETA Tool) [36mCount PASS variants[0m
[32m CountVariants [36mCounts variant records in a VCF file, regardless of filter status.[0m
[32m CountVariantsSpark [36mCountVariants on Spark[0m
[32m EvaluateInfoFieldConcordance [31m(BETA Tool) [36mEvaluate concordance of info fields in an input VCF against a validated truth VCF[0m
[32m FilterFuncotations [31m(EXPERIMENTAL Tool) [36mFilter variants based on clinically-significant Funcotations.[0m
[32m FindMendelianViolations (Picard) [36mFinds mendelian violations of all types within a VCF[0m
[32m FuncotateSegments [31m(BETA Tool) [36mFunctional annotation for segment files. The output formats are not well-defined and subject to change.[0m
[32m Funcotator [36mFunctional Annotator[0m
[32m FuncotatorDataSourceDownloader [36mData source downloader for Funcotator.[0m
[32m GenotypeConcordance (Picard) [36mCalculates the concordance between genotype data of one sample in each of two VCFs - truth (or reference) vs. calls.[0m
[32m MergeMutect2CallsWithMC3 [31m(EXPERIMENTAL Tool) [36mUNSUPPORTED. FOR EVALUATION ONLY. Merge M2 calls with MC[0m
[32m ReferenceBlockConcordance [36mEvaluate GVCF reference block concordance of an input GVCF against a truth GVCF[0m
[32m ValidateBasicSomaticShortMutations [31m(EXPERIMENTAL Tool) [36mCheck variants against tumor-normal bams representing the same samples, though not the ones from the actual calls.[0m
[32m ValidateVariants [36mValidate VCF[0m
[32m VariantEval [31m(BETA Tool) [36mGeneral-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more)[0m
[32m VariantsToTable [36mExtract fields from a VCF file to a tab-delimited table[0m
[37m--------------------------------------------------------------------------------------
[0m[31mVariant Filtering: Tools that filter variants by annotating the FILTER column[0m
[32m ApplyVQSR [36m Apply a score cutoff to filter variants based on a recalibration table[0m
[32m CNNScoreVariants [36mApply a Convolutional Neural Net to filter annotated variants[0m
[32m CNNVariantTrain [31m(EXPERIMENTAL Tool) [36mTrain a CNN model for filtering variants[0m
[32m CNNVariantWriteTensors [31m(EXPERIMENTAL Tool) [36mWrite variant tensors for training a CNN to filter variants[0m
[32m CreateSomaticPanelOfNormals [31m(BETA Tool) [36mMake a panel of normals for use with Mutect2[0m
[32m ExtractVariantAnnotations [31m(BETA Tool) [36mExtracts site-level variant annotations, labels, and other metadata from a VCF file to HDF5 files[0m
[32m FilterAlignmentArtifacts [31m(EXPERIMENTAL Tool) [36mFilter alignment artifacts from a vcf callset.[0m
[32m FilterMutectCalls [36mFilter somatic SNVs and indels called by Mutect2[0m
[32m FilterVariantTranches [36mApply tranche filtering[0m
[32m FilterVcf (Picard) [36mHard filters a VCF.[0m
[32m MTLowHeteroplasmyFilterTool [36mIf too many low het sites, filter all low het sites[0m
[32m NuMTFilterTool [36mUses the median autosomal coverage and the allele depth to determine whether the allele might be a NuMT[0m
[32m ScoreVariantAnnotations [31m(BETA Tool) [36mScores variant calls in a VCF file based on site-level annotations using a previously trained model[0m
[32m TrainVariantAnnotationsModel [31m(BETA Tool) [36mTrains a model for scoring variant calls based on site-level annotations[0m
[32m VariantFiltration [36mFilter variant calls based on INFO and/or FORMAT annotations[0m
[32m VariantRecalibrator [36mBuild a recalibration model to score variant quality for filtering purposes[0m
[37m--------------------------------------------------------------------------------------
[0m[31mVariant Manipulation: Tools that manipulate variant call format (VCF) data[0m
[32m FixVcfHeader (Picard) [36mReplaces or fixes a VCF header.[0m
[32m GatherVcfs (Picard) [36mGathers multiple VCF files from a scatter operation into a single VCF file[0m
[32m GatherVcfsCloud [31m(BETA Tool) [36mGathers multiple VCF files from a scatter operation into a single VCF file[0m
[32m LeftAlignAndTrimVariants [36mLeft align and trim vairants[0m
[32m LiftoverVcf (Picard) [36mLifts over a VCF file from one reference build to another. [0m
[32m MakeSitesOnlyVcf (Picard) [36mCreates a VCF that contains all the site-level information for all records in the input VCF but no genotype information.[0m
[32m MakeVcfSampleNameMap (Picard) [36mCreates a TSV from sample name to VCF/GVCF path, with one line per input.[0m
[32m MergeVcfs (Picard) [36mCombines multiple variant files into a single variant file[0m
[32m PrintVariantsSpark [36mPrints out variants from the input VCF.[0m
[32m RemoveNearbyIndels [36m(Internal) Remove indels from the VCF file that are close to each other.[0m
[32m RenameSampleInVcf (Picard) [36mRenames a sample within a VCF or BCF.[0m
[32m SelectVariants [36mSelect a subset of variants from a VCF file[0m
[32m SortVcf (Picard) [36mSorts one or more VCF files. [0m
[32m SplitVcfs (Picard) [36mSplits SNPs and INDELs into separate files. [0m
[32m UpdateVCFSequenceDictionary [36mUpdates the sequence dictionary in a variant file.[0m
[32m UpdateVcfSequenceDictionary (Picard) [36mTakes a VCF and a second file that contains a sequence dictionary and updates the VCF with the new sequence dictionary.[0m
[32m VariantAnnotator [36mTool for adding annotations to VCF files[0m
[32m VcfFormatConverter (Picard) [36mConverts VCF to BCF or BCF to VCF. [0m
[32m VcfToIntervalList (Picard) [36mConverts a VCF or BCF file to a Picard Interval List[0m
[37m--------------------------------------------------------------------------------------
[0m
***********************************************************************
A USER ERROR has occurred: '-Xmx104857M' is not a valid command.
***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
Using GATK jar /gatk/gatk-package-4.3.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /gatk/gatk-package-4.3.0.0-local.jar -Xmx104857M SplitNCigarReads -R input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta -I output.temp/Le1-17-502-703_1.fastq.gz_addrg_repN.bam -O output2/Le1-17-502-703_1.fastq.gz.bam
++ onerror 62
++ status=123
++ script=/yoshitake/PortablePipeline/PortablePipeline/scripts/RNA-seq~SNPcall-bbmap-callvariants
++ line=62
++ shift
++ set +x
------------------------------------------------------------
Error occured on /yoshitake/PortablePipeline/PortablePipeline/scripts/RNA-seq~SNPcall-bbmap-callvariants [Line 62]: Status 123
PID: 406241
User: yoshitake.kazutoshi
Current directory: /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants
Command line: /yoshitake/PortablePipeline/PortablePipeline/scripts/RNA-seq~SNPcall-bbmap-callvariants
------------------------------------------------------------
PID: 406239
pp runtime error.
Checking the realpath of input files.
0 input_1/
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-1-501-701_1.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-1-501-701_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-12-501-708_1.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-12-501-708_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-17-502-703_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-13-502-701_2.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-17-502-703_1.fastq.gz
1 /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/input_1/Le1-13-502-701_1.fastq.gz
0 input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
script: /yoshitake/PortablePipeline/PortablePipeline/scripts/RNA-seq~SNPcall-bbmap-callvariants "$scriptdir"/mapping-illumina~bbmap
broadinstitute/gatk:4.3.0.0 centos:centos6 quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 quay.io/biocontainers/picard:2.18.27--0
using docker
+ set -o pipefail
++ date +%s
+ time0=1677628606
+ echo start at 1677628606
start at 1677628606
++ echo input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
+ ref=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
++ echo input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
++ sed 's/[.]\(fa\|fasta\|fsa\|fna\)$//'
+ refbase=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg
+ FUNC_RUN_DOCKER quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools faidx input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
+ PP_RUN_IMAGE=quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230301_085646_962_10777
+ echo pp20230301_085646_962_10777
++ id -u
++ id -g
+ docker run --name pp20230301_085646_962_10777 -v /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants:/yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants -w /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools faidx input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta
+ rm -f input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.dict
+ FUNC_RUN_DOCKER quay.io/biocontainers/picard:2.18.27--0 picard -Xmx104857M CreateSequenceDictionary R=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta O=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.dict
+ PP_RUN_IMAGE=quay.io/biocontainers/picard:2.18.27--0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230301_085647_842_32484
+ echo pp20230301_085647_842_32484
++ id -u
++ id -g
+ docker run --name pp20230301_085647_842_32484 -v /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants:/yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants -w /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants -u 2007:600 -i --rm quay.io/biocontainers/picard:2.18.27--0 picard -Xmx104857M CreateSequenceDictionary R=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta O=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.dict
/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
INFO 2023-02-28 23:56:48 CreateSequenceDictionary
********** NOTE: Picard's command line syntax is changing.
**********
********** For more information, please see:
********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
**********
********** The command line looks like this in the new syntax:
**********
********** CreateSequenceDictionary -R input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta -O input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.dict
**********
23:56:49.237 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/picard-2.18.27-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Tue Feb 28 23:56:49 GMT 2023] CreateSequenceDictionary OUTPUT=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.dict REFERENCE=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Tue Feb 28 23:56:49 GMT 2023] Executing as ?@1efc84b0078e on Linux 3.10.0-1160.36.2.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.27-SNAPSHOT
[Tue Feb 28 23:56:49 GMT 2023] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2147483648
+ cat
+ mkdir -p output.temp output2
+ ls output/Le1-1-501-701_1.fastq.gz.bam output/Le1-12-501-708_1.fastq.gz.bam output/Le1-13-502-701_1.fastq.gz.bam output/Le1-17-502-703_1.fastq.gz.bam
+ read i
+ xargs '-d\n' -I '{}' -P 1 bash -c '{}'
++ basename output/Le1-1-501-701_1.fastq.gz.bam .bam
+ j=Le1-1-501-701_1.fastq.gz
+ echo -n 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/picard:2.18.27--0 picard -Xmx104857M AddOrReplaceReadGroups I="output/Le1-1-501-701_1.fastq.gz.bam" O=output.temp/"Le1-1-501-701_1.fastq.gz"_addrg.bam SO=coordinate RGID="Le1-1-501-701_1.fastq.gz" RGLB=library RGPL=Illumina RGPU=Illumina RGSM="Le1-1-501-701_1.fastq.gz"; '
+ echo -n '(PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools view -h output.temp/"Le1-1-501-701_1.fastq.gz"_addrg.bam)|bash run-awk-replace.sh|(PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools view -Sb -o output.temp/"Le1-1-501-701_1.fastq.gz"_addrg_repN.bam); '
+ echo -n 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools index output.temp/"Le1-1-501-701_1.fastq.gz"_addrg_repN.bam; '
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm broadinstitute/gatk:4.3.0.0 gatk --java-options -Xmx104857M SplitNCigarReads -R "input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta" -I output.temp/"Le1-1-501-701_1.fastq.gz"_addrg_repN.bam -O output2/"Le1-1-501-701_1.fastq.gz".bam'
+ read i
++ basename output/Le1-12-501-708_1.fastq.gz.bam .bam
+ j=Le1-12-501-708_1.fastq.gz
+ echo -n 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/picard:2.18.27--0 picard -Xmx104857M AddOrReplaceReadGroups I="output/Le1-12-501-708_1.fastq.gz.bam" O=output.temp/"Le1-12-501-708_1.fastq.gz"_addrg.bam SO=coordinate RGID="Le1-12-501-708_1.fastq.gz" RGLB=library RGPL=Illumina RGPU=Illumina RGSM="Le1-12-501-708_1.fastq.gz"; '
+ echo -n '(PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools view -h output.temp/"Le1-12-501-708_1.fastq.gz"_addrg.bam)|bash run-awk-replace.sh|(PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools view -Sb -o output.temp/"Le1-12-501-708_1.fastq.gz"_addrg_repN.bam); '
+ echo -n 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools index output.temp/"Le1-12-501-708_1.fastq.gz"_addrg_repN.bam; '
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm broadinstitute/gatk:4.3.0.0 gatk --java-options -Xmx104857M SplitNCigarReads -R "input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta" -I output.temp/"Le1-12-501-708_1.fastq.gz"_addrg_repN.bam -O output2/"Le1-12-501-708_1.fastq.gz".bam'
+ read i
++ basename output/Le1-13-502-701_1.fastq.gz.bam .bam
+ j=Le1-13-502-701_1.fastq.gz
+ echo -n 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/picard:2.18.27--0 picard -Xmx104857M AddOrReplaceReadGroups I="output/Le1-13-502-701_1.fastq.gz.bam" O=output.temp/"Le1-13-502-701_1.fastq.gz"_addrg.bam SO=coordinate RGID="Le1-13-502-701_1.fastq.gz" RGLB=library RGPL=Illumina RGPU=Illumina RGSM="Le1-13-502-701_1.fastq.gz"; '
+ echo -n '(PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools view -h output.temp/"Le1-13-502-701_1.fastq.gz"_addrg.bam)|bash run-awk-replace.sh|(PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools view -Sb -o output.temp/"Le1-13-502-701_1.fastq.gz"_addrg_repN.bam); '
+ echo -n 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools index output.temp/"Le1-13-502-701_1.fastq.gz"_addrg_repN.bam; '
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm broadinstitute/gatk:4.3.0.0 gatk --java-options -Xmx104857M SplitNCigarReads -R "input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta" -I output.temp/"Le1-13-502-701_1.fastq.gz"_addrg_repN.bam -O output2/"Le1-13-502-701_1.fastq.gz".bam'
+ read i
++ basename output/Le1-17-502-703_1.fastq.gz.bam .bam
+ j=Le1-17-502-703_1.fastq.gz
+ echo -n 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/picard:2.18.27--0 picard -Xmx104857M AddOrReplaceReadGroups I="output/Le1-17-502-703_1.fastq.gz.bam" O=output.temp/"Le1-17-502-703_1.fastq.gz"_addrg.bam SO=coordinate RGID="Le1-17-502-703_1.fastq.gz" RGLB=library RGPL=Illumina RGPU=Illumina RGSM="Le1-17-502-703_1.fastq.gz"; '
+ echo -n '(PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools view -h output.temp/"Le1-17-502-703_1.fastq.gz"_addrg.bam)|bash run-awk-replace.sh|(PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools view -Sb -o output.temp/"Le1-17-502-703_1.fastq.gz"_addrg_repN.bam); '
+ echo -n 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 samtools index output.temp/"Le1-17-502-703_1.fastq.gz"_addrg_repN.bam; '
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm broadinstitute/gatk:4.3.0.0 gatk --java-options -Xmx104857M SplitNCigarReads -R "input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta" -I output.temp/"Le1-17-502-703_1.fastq.gz"_addrg_repN.bam -O output2/"Le1-17-502-703_1.fastq.gz".bam'
+ read i
/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
INFO 2023-02-28 23:56:50 AddOrReplaceReadGroups
********** NOTE: Picard's command line syntax is changing.
**********
********** For more information, please see:
********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
**********
********** The command line looks like this in the new syntax:
**********
********** AddOrReplaceReadGroups -I output/Le1-1-501-701_1.fastq.gz.bam -O output.temp/Le1-1-501-701_1.fastq.gz_addrg.bam -SO coordinate -RGID Le1-1-501-701_1.fastq.gz -RGLB library -RGPL Illumina -RGPU Illumina -RGSM Le1-1-501-701_1.fastq.gz
**********
23:56:51.350 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/picard-2.18.27-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Tue Feb 28 23:56:51 GMT 2023] AddOrReplaceReadGroups INPUT=output/Le1-1-501-701_1.fastq.gz.bam OUTPUT=output.temp/Le1-1-501-701_1.fastq.gz_addrg.bam SORT_ORDER=coordinate RGID=Le1-1-501-701_1.fastq.gz RGLB=library RGPL=Illumina RGPU=Illumina RGSM=Le1-1-501-701_1.fastq.gz VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Tue Feb 28 23:56:51 GMT 2023] Executing as ?@a7e757820c00 on Linux 3.10.0-1160.36.2.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.27-SNAPSHOT
INFO 2023-02-28 23:56:51 AddOrReplaceReadGroups Created read-group ID=Le1-1-501-701_1.fastq.gz PL=Illumina LB=library SM=Le1-1-501-701_1.fastq.gz
[Tue Feb 28 23:56:54 GMT 2023] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=2617245696
23:57:02.083 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
23:57:02.265 INFO SplitNCigarReads - ------------------------------------------------------------
23:57:02.266 INFO SplitNCigarReads - The Genome Analysis Toolkit (GATK) v4.3.0.0
23:57:02.266 INFO SplitNCigarReads - For support and documentation go to https://software.broadinstitute.org/gatk/
23:57:02.267 INFO SplitNCigarReads - Executing as ?@190270ec2003 on Linux v3.10.0-1160.36.2.el7.x86_64 amd64
23:57:02.267 INFO SplitNCigarReads - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-8u242-b08-0ubuntu3~18.04-b08
23:57:02.267 INFO SplitNCigarReads - Start Date/Time: February 28, 2023 11:57:02 PM GMT
23:57:02.268 INFO SplitNCigarReads - ------------------------------------------------------------
23:57:02.268 INFO SplitNCigarReads - ------------------------------------------------------------
23:57:02.269 INFO SplitNCigarReads - HTSJDK Version: 3.0.1
23:57:02.269 INFO SplitNCigarReads - Picard Version: 2.27.5
23:57:02.269 INFO SplitNCigarReads - Built for Spark Version: 2.4.5
23:57:02.270 INFO SplitNCigarReads - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:57:02.270 INFO SplitNCigarReads - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:57:02.270 INFO SplitNCigarReads - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:57:02.270 INFO SplitNCigarReads - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:57:02.270 INFO SplitNCigarReads - Deflater: IntelDeflater
23:57:02.271 INFO SplitNCigarReads - Inflater: IntelInflater
23:57:02.271 INFO SplitNCigarReads - GCS max retries/reopens: 20
23:57:02.271 INFO SplitNCigarReads - Requester pays: disabled
23:57:02.271 INFO SplitNCigarReads - Initializing engine
23:57:02.636 INFO SplitNCigarReads - Done initializing engine
23:57:02.682 INFO ProgressMeter - Starting traversal
23:57:02.682 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
23:57:04.595 WARN IntelInflater - Zero Bytes Written : 0
23:57:04.598 INFO SplitNCigarReads - 0 read(s) filtered by: AllowAllReadsReadFilter
23:57:04.599 INFO OverhangFixingManager - Overhang Fixing Manager saved 512 reads in the first pass
23:57:04.601 INFO SplitNCigarReads - Starting traversal pass 2
23:57:06.700 WARN IntelInflater - Zero Bytes Written : 0
23:57:06.701 INFO SplitNCigarReads - 0 read(s) filtered by: AllowAllReadsReadFilter
23:57:06.702 INFO ProgressMeter - h1tg000096l:21503 0.1 291848 4357024.1
23:57:06.702 INFO ProgressMeter - Traversal complete. Processed 291848 total reads in 0.1 minutes.
23:57:07.655 INFO SplitNCigarReads - Shutting down engine
[February 28, 2023 11:57:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=2649751552
Using GATK jar /gatk/gatk-package-4.3.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx104857M -jar /gatk/gatk-package-4.3.0.0-local.jar SplitNCigarReads -R input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta -I output.temp/Le1-1-501-701_1.fastq.gz_addrg_repN.bam -O output2/Le1-1-501-701_1.fastq.gz.bam
/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
INFO 2023-02-28 23:57:09 AddOrReplaceReadGroups
********** NOTE: Picard's command line syntax is changing.
**********
********** For more information, please see:
********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
**********
********** The command line looks like this in the new syntax:
**********
********** AddOrReplaceReadGroups -I output/Le1-12-501-708_1.fastq.gz.bam -O output.temp/Le1-12-501-708_1.fastq.gz_addrg.bam -SO coordinate -RGID Le1-12-501-708_1.fastq.gz -RGLB library -RGPL Illumina -RGPU Illumina -RGSM Le1-12-501-708_1.fastq.gz
**********
23:57:09.474 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/picard-2.18.27-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Tue Feb 28 23:57:09 GMT 2023] AddOrReplaceReadGroups INPUT=output/Le1-12-501-708_1.fastq.gz.bam OUTPUT=output.temp/Le1-12-501-708_1.fastq.gz_addrg.bam SORT_ORDER=coordinate RGID=Le1-12-501-708_1.fastq.gz RGLB=library RGPL=Illumina RGPU=Illumina RGSM=Le1-12-501-708_1.fastq.gz VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Tue Feb 28 23:57:09 GMT 2023] Executing as ?@8ed77b40bd2d on Linux 3.10.0-1160.36.2.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.27-SNAPSHOT
INFO 2023-02-28 23:57:09 AddOrReplaceReadGroups Created read-group ID=Le1-12-501-708_1.fastq.gz PL=Illumina LB=library SM=Le1-12-501-708_1.fastq.gz
[Tue Feb 28 23:57:10 GMT 2023] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2147483648
23:57:15.597 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
23:57:15.754 INFO SplitNCigarReads - ------------------------------------------------------------
23:57:15.755 INFO SplitNCigarReads - The Genome Analysis Toolkit (GATK) v4.3.0.0
23:57:15.755 INFO SplitNCigarReads - For support and documentation go to https://software.broadinstitute.org/gatk/
23:57:15.755 INFO SplitNCigarReads - Executing as ?@bb566256d80e on Linux v3.10.0-1160.36.2.el7.x86_64 amd64
23:57:15.756 INFO SplitNCigarReads - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-8u242-b08-0ubuntu3~18.04-b08
23:57:15.756 INFO SplitNCigarReads - Start Date/Time: February 28, 2023 11:57:15 PM GMT
23:57:15.756 INFO SplitNCigarReads - ------------------------------------------------------------
23:57:15.756 INFO SplitNCigarReads - ------------------------------------------------------------
23:57:15.757 INFO SplitNCigarReads - HTSJDK Version: 3.0.1
23:57:15.757 INFO SplitNCigarReads - Picard Version: 2.27.5
23:57:15.757 INFO SplitNCigarReads - Built for Spark Version: 2.4.5
23:57:15.757 INFO SplitNCigarReads - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:57:15.757 INFO SplitNCigarReads - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:57:15.757 INFO SplitNCigarReads - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:57:15.758 INFO SplitNCigarReads - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:57:15.758 INFO SplitNCigarReads - Deflater: IntelDeflater
23:57:15.758 INFO SplitNCigarReads - Inflater: IntelInflater
23:57:15.758 INFO SplitNCigarReads - GCS max retries/reopens: 20
23:57:15.758 INFO SplitNCigarReads - Requester pays: disabled
23:57:15.758 INFO SplitNCigarReads - Initializing engine
23:57:16.123 INFO SplitNCigarReads - Done initializing engine
23:57:16.170 INFO ProgressMeter - Starting traversal
23:57:16.171 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
23:57:16.973 WARN IntelInflater - Zero Bytes Written : 0
23:57:16.976 INFO SplitNCigarReads - 0 read(s) filtered by: AllowAllReadsReadFilter
23:57:16.976 INFO OverhangFixingManager - Overhang Fixing Manager saved 54 reads in the first pass
23:57:16.979 INFO SplitNCigarReads - Starting traversal pass 2
23:57:17.468 WARN IntelInflater - Zero Bytes Written : 0
23:57:17.469 INFO SplitNCigarReads - 0 read(s) filtered by: AllowAllReadsReadFilter
23:57:17.470 INFO ProgressMeter - h1tg000069l:128641 0.0 36932 1707180.3
23:57:17.471 INFO ProgressMeter - Traversal complete. Processed 36932 total reads in 0.0 minutes.
23:57:17.720 INFO SplitNCigarReads - Shutting down engine
[February 28, 2023 11:57:17 PM GMT] org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=2528641024
Using GATK jar /gatk/gatk-package-4.3.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx104857M -jar /gatk/gatk-package-4.3.0.0-local.jar SplitNCigarReads -R input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta -I output.temp/Le1-12-501-708_1.fastq.gz_addrg_repN.bam -O output2/Le1-12-501-708_1.fastq.gz.bam
/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
INFO 2023-02-28 23:57:18 AddOrReplaceReadGroups
********** NOTE: Picard's command line syntax is changing.
**********
********** For more information, please see:
********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
**********
********** The command line looks like this in the new syntax:
**********
********** AddOrReplaceReadGroups -I output/Le1-13-502-701_1.fastq.gz.bam -O output.temp/Le1-13-502-701_1.fastq.gz_addrg.bam -SO coordinate -RGID Le1-13-502-701_1.fastq.gz -RGLB library -RGPL Illumina -RGPU Illumina -RGSM Le1-13-502-701_1.fastq.gz
**********
23:57:19.401 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/picard-2.18.27-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Tue Feb 28 23:57:19 GMT 2023] AddOrReplaceReadGroups INPUT=output/Le1-13-502-701_1.fastq.gz.bam OUTPUT=output.temp/Le1-13-502-701_1.fastq.gz_addrg.bam SORT_ORDER=coordinate RGID=Le1-13-502-701_1.fastq.gz RGLB=library RGPL=Illumina RGPU=Illumina RGSM=Le1-13-502-701_1.fastq.gz VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Tue Feb 28 23:57:19 GMT 2023] Executing as ?@8b08e65aee13 on Linux 3.10.0-1160.36.2.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.27-SNAPSHOT
INFO 2023-02-28 23:57:19 AddOrReplaceReadGroups Created read-group ID=Le1-13-502-701_1.fastq.gz PL=Illumina LB=library SM=Le1-13-502-701_1.fastq.gz
[Tue Feb 28 23:57:24 GMT 2023] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=2650800128
23:57:33.470 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
23:57:33.619 INFO SplitNCigarReads - ------------------------------------------------------------
23:57:33.619 INFO SplitNCigarReads - The Genome Analysis Toolkit (GATK) v4.3.0.0
23:57:33.619 INFO SplitNCigarReads - For support and documentation go to https://software.broadinstitute.org/gatk/
23:57:33.619 INFO SplitNCigarReads - Executing as ?@d4eecf8c91c6 on Linux v3.10.0-1160.36.2.el7.x86_64 amd64
23:57:33.620 INFO SplitNCigarReads - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-8u242-b08-0ubuntu3~18.04-b08
23:57:33.620 INFO SplitNCigarReads - Start Date/Time: February 28, 2023 11:57:33 PM GMT
23:57:33.620 INFO SplitNCigarReads - ------------------------------------------------------------
23:57:33.620 INFO SplitNCigarReads - ------------------------------------------------------------
23:57:33.621 INFO SplitNCigarReads - HTSJDK Version: 3.0.1
23:57:33.621 INFO SplitNCigarReads - Picard Version: 2.27.5
23:57:33.621 INFO SplitNCigarReads - Built for Spark Version: 2.4.5
23:57:33.621 INFO SplitNCigarReads - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:57:33.621 INFO SplitNCigarReads - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:57:33.621 INFO SplitNCigarReads - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:57:33.621 INFO SplitNCigarReads - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:57:33.621 INFO SplitNCigarReads - Deflater: IntelDeflater
23:57:33.621 INFO SplitNCigarReads - Inflater: IntelInflater
23:57:33.621 INFO SplitNCigarReads - GCS max retries/reopens: 20
23:57:33.621 INFO SplitNCigarReads - Requester pays: disabled
23:57:33.621 INFO SplitNCigarReads - Initializing engine
23:57:33.964 INFO SplitNCigarReads - Done initializing engine
23:57:34.001 INFO ProgressMeter - Starting traversal
23:57:34.002 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
23:57:37.245 WARN IntelInflater - Zero Bytes Written : 0
23:57:37.247 INFO SplitNCigarReads - 0 read(s) filtered by: AllowAllReadsReadFilter
23:57:37.248 INFO OverhangFixingManager - Overhang Fixing Manager saved 1984 reads in the first pass
23:57:37.250 INFO SplitNCigarReads - Starting traversal pass 2
23:57:40.982 WARN IntelInflater - Zero Bytes Written : 0
23:57:40.983 INFO SplitNCigarReads - 0 read(s) filtered by: AllowAllReadsReadFilter
23:57:40.984 INFO ProgressMeter - unmapped 0.1 491400 4223463.7
23:57:40.984 INFO ProgressMeter - Traversal complete. Processed 491400 total reads in 0.1 minutes.
23:57:42.424 INFO SplitNCigarReads - Shutting down engine
[February 28, 2023 11:57:42 PM GMT] org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=2900885504
Using GATK jar /gatk/gatk-package-4.3.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx104857M -jar /gatk/gatk-package-4.3.0.0-local.jar SplitNCigarReads -R input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta -I output.temp/Le1-13-502-701_1.fastq.gz_addrg_repN.bam -O output2/Le1-13-502-701_1.fastq.gz.bam
/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
INFO 2023-02-28 23:57:43 AddOrReplaceReadGroups
********** NOTE: Picard's command line syntax is changing.
**********
********** For more information, please see:
********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
**********
********** The command line looks like this in the new syntax:
**********
********** AddOrReplaceReadGroups -I output/Le1-17-502-703_1.fastq.gz.bam -O output.temp/Le1-17-502-703_1.fastq.gz_addrg.bam -SO coordinate -RGID Le1-17-502-703_1.fastq.gz -RGLB library -RGPL Illumina -RGPU Illumina -RGSM Le1-17-502-703_1.fastq.gz
**********
23:57:44.226 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/picard-2.18.27-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Tue Feb 28 23:57:44 GMT 2023] AddOrReplaceReadGroups INPUT=output/Le1-17-502-703_1.fastq.gz.bam OUTPUT=output.temp/Le1-17-502-703_1.fastq.gz_addrg.bam SORT_ORDER=coordinate RGID=Le1-17-502-703_1.fastq.gz RGLB=library RGPL=Illumina RGPU=Illumina RGSM=Le1-17-502-703_1.fastq.gz VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Tue Feb 28 23:57:44 GMT 2023] Executing as ?@71e2a21c6f0b on Linux 3.10.0-1160.36.2.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.27-SNAPSHOT
INFO 2023-02-28 23:57:44 AddOrReplaceReadGroups Created read-group ID=Le1-17-502-703_1.fastq.gz PL=Illumina LB=library SM=Le1-17-502-703_1.fastq.gz
[Tue Feb 28 23:57:58 GMT 2023] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 0.23 minutes.
Runtime.totalMemory()=2583691264
23:58:14.002 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
23:58:14.183 INFO SplitNCigarReads - ------------------------------------------------------------
23:58:14.184 INFO SplitNCigarReads - The Genome Analysis Toolkit (GATK) v4.3.0.0
23:58:14.184 INFO SplitNCigarReads - For support and documentation go to https://software.broadinstitute.org/gatk/
23:58:14.184 INFO SplitNCigarReads - Executing as ?@acb80e86b8fa on Linux v3.10.0-1160.36.2.el7.x86_64 amd64
23:58:14.184 INFO SplitNCigarReads - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-8u242-b08-0ubuntu3~18.04-b08
23:58:14.184 INFO SplitNCigarReads - Start Date/Time: February 28, 2023 11:58:13 PM GMT
23:58:14.185 INFO SplitNCigarReads - ------------------------------------------------------------
23:58:14.185 INFO SplitNCigarReads - ------------------------------------------------------------
23:58:14.185 INFO SplitNCigarReads - HTSJDK Version: 3.0.1
23:58:14.186 INFO SplitNCigarReads - Picard Version: 2.27.5
23:58:14.186 INFO SplitNCigarReads - Built for Spark Version: 2.4.5
23:58:14.186 INFO SplitNCigarReads - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:58:14.186 INFO SplitNCigarReads - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:58:14.186 INFO SplitNCigarReads - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:58:14.186 INFO SplitNCigarReads - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:58:14.186 INFO SplitNCigarReads - Deflater: IntelDeflater
23:58:14.186 INFO SplitNCigarReads - Inflater: IntelInflater
23:58:14.186 INFO SplitNCigarReads - GCS max retries/reopens: 20
23:58:14.186 INFO SplitNCigarReads - Requester pays: disabled
23:58:14.186 INFO SplitNCigarReads - Initializing engine
23:58:14.557 INFO SplitNCigarReads - Done initializing engine
23:58:14.607 INFO ProgressMeter - Starting traversal
23:58:14.607 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
23:58:24.475 WARN IntelInflater - Zero Bytes Written : 0
23:58:24.477 INFO SplitNCigarReads - 0 read(s) filtered by: AllowAllReadsReadFilter
23:58:24.478 INFO OverhangFixingManager - Overhang Fixing Manager saved 5569 reads in the first pass
23:58:24.479 INFO SplitNCigarReads - Starting traversal pass 2
23:58:24.616 INFO ProgressMeter - h1tg000001l:746357 0.2 695000 4167083.0
23:58:37.192 INFO ProgressMeter - h1tg000051l:135989 0.4 1240000 3294367.7
23:58:39.277 WARN IntelInflater - Zero Bytes Written : 0
23:58:39.278 INFO SplitNCigarReads - 0 read(s) filtered by: AllowAllReadsReadFilter
23:58:39.278 INFO ProgressMeter - h1tg000097l:38077 0.4 1352628 3289731.7
23:58:39.278 INFO ProgressMeter - Traversal complete. Processed 1352628 total reads in 0.4 minutes.
23:58:42.243 INFO SplitNCigarReads - Shutting down engine
[February 28, 2023 11:58:42 PM GMT] org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads done. Elapsed time: 0.47 minutes.
Runtime.totalMemory()=5519179776
Using GATK jar /gatk/gatk-package-4.3.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx104857M -jar /gatk/gatk-package-4.3.0.0-local.jar SplitNCigarReads -R input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta -I output.temp/Le1-17-502-703_1.fastq.gz_addrg_repN.bam -O output2/Le1-17-502-703_1.fastq.gz.bam
+ inputbams=
+ multiflag=
++ ls output2/Le1-1-501-701_1.fastq.gz.bam output2/Le1-12-501-708_1.fastq.gz.bam output2/Le1-13-502-701_1.fastq.gz.bam output2/Le1-17-502-703_1.fastq.gz.bam
+ for i in '`ls output2/*.bam`'
+ '[' '' = '' ']'
+ inputbams=output2/Le1-1-501-701_1.fastq.gz.bam
+ for i in '`ls output2/*.bam`'
+ '[' output2/Le1-1-501-701_1.fastq.gz.bam = '' ']'
+ multiflag=multisample=t
+ inputbams+=,output2/Le1-12-501-708_1.fastq.gz.bam
+ for i in '`ls output2/*.bam`'
+ '[' output2/Le1-1-501-701_1.fastq.gz.bam,output2/Le1-12-501-708_1.fastq.gz.bam = '' ']'
+ multiflag=multisample=t
+ inputbams+=,output2/Le1-13-502-701_1.fastq.gz.bam
+ for i in '`ls output2/*.bam`'
+ '[' output2/Le1-1-501-701_1.fastq.gz.bam,output2/Le1-12-501-708_1.fastq.gz.bam,output2/Le1-13-502-701_1.fastq.gz.bam = '' ']'
+ multiflag=multisample=t
+ inputbams+=,output2/Le1-17-502-703_1.fastq.gz.bam
+ FUNC_RUN_DOCKER quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 callvariants.sh -Xmx104857M in=output2/Le1-1-501-701_1.fastq.gz.bam,output2/Le1-12-501-708_1.fastq.gz.bam,output2/Le1-13-502-701_1.fastq.gz.bam,output2/Le1-17-502-703_1.fastq.gz.bam ref=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta vcf=output.vcf multisample=t ploidy=2
+ PP_RUN_IMAGE=quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230301_085842_649_26537
+ echo pp20230301_085842_649_26537
++ id -u
++ id -g
+ docker run --name pp20230301_085842_649_26537 -v /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants:/yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants -w /yoshitake/test/RNA-seq~SNPcall-bbmap-callvariants -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 callvariants.sh -Xmx104857M in=output2/Le1-1-501-701_1.fastq.gz.bam,output2/Le1-12-501-708_1.fastq.gz.bam,output2/Le1-13-502-701_1.fastq.gz.bam,output2/Le1-17-502-703_1.fastq.gz.bam ref=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta vcf=output.vcf multisample=t ploidy=2
java -ea -Xmx104857M -Xms104857M -cp /usr/local/opt/bbmap-38.96-1/current/ var2.CallVariants -Xmx104857M in=output2/Le1-1-501-701_1.fastq.gz.bam,output2/Le1-12-501-708_1.fastq.gz.bam,output2/Le1-13-502-701_1.fastq.gz.bam,output2/Le1-17-502-703_1.fastq.gz.bam ref=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta vcf=output.vcf multisample=t ploidy=2
Executing var2.CallVariants2 [-Xmx104857M, in=output2/Le1-1-501-701_1.fastq.gz.bam,output2/Le1-12-501-708_1.fastq.gz.bam,output2/Le1-13-502-701_1.fastq.gz.bam,output2/Le1-17-502-703_1.fastq.gz.bam, ref=input_2/Shiitake_XR1.asm.bp.hap1.p_ctg.fasta, vcf=output.vcf, multisample=t, ploidy=2]
Calculating which variants pass filters.
Processing sample Le1-1-501-701_1.
Loading variants.
Could not find sambamba.
Found samtools 1.15
Time: 1.830 seconds.
Processing variants.
Time: 0.234 seconds.
Counting nearby variants.
Time: 0.065 seconds.
Processing sample Le1-12-501-708_1.
Loading variants.
Time: 0.087 seconds.
Processing variants.
Time: 0.020 seconds.
Counting nearby variants.
Time: 0.003 seconds.
Processing sample Le1-13-502-701_1.
Loading variants.
Time: 0.484 seconds.
Processing variants.
Time: 0.047 seconds.
Counting nearby variants.
Time: 0.032 seconds.
Processing sample Le1-17-502-703_1.
Loading variants.
Time: 1.155 seconds.
Processing variants.
Time: 0.182 seconds.
Counting nearby variants.
Time: 0.107 seconds.
100676 variants passed filters. 4.370 seconds.
Processing second pass.
Processing sample Le1-1-501-701_1.
Loading variants.
Time: 0.366 seconds.
Processing variants.
Time: 0.195 seconds.
Processing sample Le1-12-501-708_1.
Loading variants.
Time: 0.115 seconds.
Processing variants.
Time: 0.085 seconds.
Processing sample Le1-13-502-701_1.
Loading variants.
Time: 0.435 seconds.
Processing variants.
Time: 0.083 seconds.
Processing sample Le1-17-502-703_1.
Loading variants.
Time: 1.151 seconds.
Processing variants.
Time: 0.118 seconds.
Finished second pass.
Writing output.
Merging [(Le1-1-501-701_1, individual_Le1-1-501-701_1.vcf.gz), (Le1-12-501-708_1, individual_Le1-12-501-708_1.vcf.gz), (Le1-13-502-701_1, individual_Le1-13-502-701_1.vcf.gz), (Le1-17-502-703_1, individual_Le1-17-502-703_1.vcf.gz)]
Time: 1.531 seconds.
100676 of 1912649 variants passed filters (5.2637%).
Substitutions: 90317 89.7%
Deletions: 5743 5.7%
Insertions: 4616 4.6%
Variation Rate: 1/539
Time: 10.320 seconds.
Reads Processed: 1034k 100.27k reads/sec
Bases Processed: 156m 15.14m bases/sec
++ date
+ echo completion at 2023年 3月 1日 水曜日 08:58:54 JST
completion at 2023年 3月 1日 水曜日 08:58:54 JST
++ date +%s
+ time_fin=1677628734
++ echo 'scale=2; (1677628734 - 1677628606)/60'
++ bc
+ echo -e 'Total running time is 2.13 min'
Total running time is 2.13 min
+ echo 'Run completed!'
Run completed!
+ post_processing
+ '[' 1 = 1 ']'
+ echo 0
+ exit
PID: 412203