+ 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