miRDeep2 mapping for small RNA reads.
@V350167022L2C001R00100001856
AAATGCAGTCAGGTAAAGATGGCAGTCGGAGCCCAAGCGGTCTTAGCAAG
+
B)>587#5A72F@<ACB,(DDD=;E99AAAE8BFC1BC;B,D>2B6'CC8
@V350167022L2C001R00100011397
CAACCGTCGGAGCCCAAGCGGACTTAGGAAGTCAATAGGTCCGATCAACT
+
ADDG'D9@;EEE2C.CBGF?>?E5AEFCAEE(D?D0C)@D36*$/=BD5B
@V350167022L2C001R00100013275
TATCACAGCCAGCTTTGATGAGCTAGTCGGAGTCCAAGCGGACTTAGGAA
mapping-smallRNA-miRDeep2 -c 8 -m 32 input_1/ input_2/pfu4A-B_birnaA-B.fa input_3/
seq_0_x1025 50 1 50 atggaaggtccggagagtctaggttacccaattcaattcgatacttcaat v4.1_scaf_03b 50 16673756 16673805 atggaaggtccggagagtctaggttacccaattcaattcgatacttcaat + 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_0_x1025 50 1 50 atggaaggtccggagagtctaggttacccaattcaattcgatacttcaat v4.1_scaf_03a 50 16819294 16819343 atggaaggtccggagagtctaggttacccaattcaattcgatacttcaat + 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_1025_x742 50 1 50 caactctaagcggtggatcactcggctcgtgcgtcgatgaagagcgcagc v4.1_scaf_04b 50 70733729 70733778 caactctaagcggtggatcactcggctcgtgcgtcgatgaagagcgcagc + 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_1025_x742 50 1 50 caactctaagcggtggatcactcggctcgtgcgtcgatgaagagcgcagc v4.1_scaf_04b 50 70714957 70715006 caactctaagcggtggatcactcggctcgtgcgtcgatgaagagcgcagc + 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_1025_x742 50 1 50 caactctaagcggtggatcactcggctcgtgcgtcgatgaagagcgcagc v4.1_scaf_04b 50 70686812 70686861 caactctaagcggtggatcactcggctcgtgcgtcgatgaagagcgcagc + 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_1025_x742 50 1 50 caactctaagcggtggatcactcggctcgtgcgtcgatgaagagcgcagc v4.1_scaf_04b 50 70696193 70696242 caactctaagcggtggatcactcggctcgtgcgtcgatgaagagcgcagc + 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_1025_x742 50 1 50 caactctaagcggtggatcactcggctcgtgcgtcgatgaagagcgcagc v4.1_scaf_04b 50 70705574 70705623 caactctaagcggtggatcactcggctcgtgcgtcgatgaagagcgcagc + 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_1025_x742 50 1 50 caactctaagcggtggatcactcggctcgtgcgtcgatgaagagcgcagc v4.1_scaf_04b 50 70724339 70724388 caactctaagcggtggatcactcggctcgtgcgtcgatgaagagcgcagc + 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_1767_x236 49 1 49 tggaaggtccggagagtctaggttacccaattcaattcgatacttcaat v4.1_scaf_03b 49 16673757 16673805 tggaaggtccggagagtctaggttacccaattcaattcgatacttcaat + 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_1767_x236 49 1 49 tggaaggtccggagagtctaggttacccaattcaattcgatacttcaat v4.1_scaf_03a 49 16819295 16819343 tggaaggtccggagagtctaggttacccaattcaattcgatacttcaat + 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_0_x771 50 1 50 atggaaggtccggagagtctaggttacccaattcaattcgatacttcaat v4.1_scaf_03b 50 16673756 16673805 atggaaggtccggagagtctaggttacccaattcaattcgatacttcaat + 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_0_x771 50 1 50 atggaaggtccggagagtctaggttacccaattcaattcgatacttcaat v4.1_scaf_03a 50 16819294 16819343 atggaaggtccggagagtctaggttacccaattcaattcgatacttcaat + 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_771_x589 50 1 50 caactctaagcggtggatcactcggctcgtgcgtcgatgaagagcgcagc v4.1_scaf_04b 50 70686812 70686861 caactctaagcggtggatcactcggctcgtgcgtcgatgaagagcgcagc + 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_771_x589 50 1 50 caactctaagcggtggatcactcggctcgtgcgtcgatgaagagcgcagc v4.1_scaf_04b 50 70696193 70696242 caactctaagcggtggatcactcggctcgtgcgtcgatgaagagcgcagc + 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_771_x589 50 1 50 caactctaagcggtggatcactcggctcgtgcgtcgatgaagagcgcagc v4.1_scaf_04b 50 70705574 70705623 caactctaagcggtggatcactcggctcgtgcgtcgatgaagagcgcagc + 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_771_x589 50 1 50 caactctaagcggtggatcactcggctcgtgcgtcgatgaagagcgcagc v4.1_scaf_04b 50 70724339 70724388 caactctaagcggtggatcactcggctcgtgcgtcgatgaagagcgcagc + 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_771_x589 50 1 50 caactctaagcggtggatcactcggctcgtgcgtcgatgaagagcgcagc v4.1_scaf_04b 50 70733729 70733778 caactctaagcggtggatcactcggctcgtgcgtcgatgaagagcgcagc + 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_771_x589 50 1 50 caactctaagcggtggatcactcggctcgtgcgtcgatgaagagcgcagc v4.1_scaf_04b 50 70714957 70715006 caactctaagcggtggatcactcggctcgtgcgtcgatgaagagcgcagc + 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_1360_x309 22 1 22 tgaggtagtaggttgtatagtt v4.1_scaf_09b 22 27240674 27240695 tgaggtagtaggttgtatagtt + 0 mmmmmmmmmmmmmmmmmmmmmm
seq_1360_x309 22 1 22 tgaggtagtaggttgtatagtt v4.1_scaf_09a 22 27959835 27959856 tgaggtagtaggttgtatagtt + 0 mmmmmmmmmmmmmmmmmmmmmm
pp mapping-smallRNA-miRDeep2 -c 8 -m 32 input_1/ input_2/pfu4A-B_birnaA-B.fa input_3/
PID: 1444323
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/pp mapping-smallRNA-miRDeep2 -c 8 -m 32 input_1/ input_2/pfu4A-B_birnaA-B.fa input_3/
Checking the realpath of input files.
1
c2997108/mirdeep2:1 centos:centos6
using docker
+ set -o pipefail
+ '[' input_3/ = '' ']'
++ ls -LS input_3//pfu4A-B_birnaA-B.fa.1.ebwt input_3//pfu4A-B_birnaA-B.fa.2.ebwt input_3//pfu4A-B_birnaA-B.fa.3.ebwt input_3//pfu4A-B_birnaA-B.fa.4.ebwt input_3//pfu4A-B_birnaA-B.fa.rev.1.ebwt input_3//pfu4A-B_birnaA-B.fa.rev.2.ebwt
++ grep '[.]1[.]ebwt$'
++ head -n 1
++ sed 's/.1.ebwt$//'
+ input_2=input_3//pfu4A-B_birnaA-B.fa
+ mkdir -p fastq.gunzip
+ xargs '-d\n' -I '{}' -P 1 bash -c '{}'
++ find input_1// -maxdepth 1
++ grep -E '[.](fastq|fq)[.]gz$'
+ for i in `find "$input_1"/ -maxdepth 1 |grep -E '[.](fastq|fq)[.]gz$' || true`
++ basename input_1//3day-1.fq.gz .gz
+ echo DO_MIRDEEP2 'zcat input_1//3day-1.fq.gz > fastq.gunzip/3day-1.fq'
bash: DO_MIRDEEP2: command not found
++ onerror 39
++ status=123
++ script=/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/mapping-smallRNA-miRDeep2
++ line=39
++ shift
++ set +x
------------------------------------------------------------
Error occured on /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/mapping-smallRNA-miRDeep2 [Line 39]: Status 123
PID: 1444325
User: yoshitake.kazutoshi
Current directory: /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-smallRNA-miRDeep2
Command line: /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/mapping-smallRNA-miRDeep2
------------------------------------------------------------
PID: 1448554
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/pp mapping-smallRNA-miRDeep2 -c 8 -m 32 input_1/ input_2/pfu4A-B_birnaA-B.fa input_3/
Checking the realpath of input files.
1
c2997108/mirdeep2:1 centos:centos6
using docker
+ set -o pipefail
+ '[' input_3/ = '' ']'
++ ls -LS input_3//pfu4A-B_birnaA-B.fa.1.ebwt input_3//pfu4A-B_birnaA-B.fa.2.ebwt input_3//pfu4A-B_birnaA-B.fa.3.ebwt input_3//pfu4A-B_birnaA-B.fa.4.ebwt input_3//pfu4A-B_birnaA-B.fa.rev.1.ebwt input_3//pfu4A-B_birnaA-B.fa.rev.2.ebwt
++ grep '[.]1[.]ebwt$'
++ head -n 1
++ sed 's/.1.ebwt$//'
+ input_2=input_3//pfu4A-B_birnaA-B.fa
+ mkdir -p fastq.gunzip
+ xargs '-d\n' -I '{}' -P 1 bash -c '{}'
++ find input_1// -maxdepth 1
++ grep -E '[.](fastq|fq)[.]gz$'
+ for i in `find "$input_1"/ -maxdepth 1 |grep -E '[.](fastq|fq)[.]gz$' || true`
++ basename input_1//3day-1.fq.gz .gz
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-smallRNA-miRDeep2/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi:/data/yoshitake.kazutoshi -v /suikou/files/m768/yoshitake.kazutoshi/work/smallrna/matsuyama:/suikou/files/m768/yoshitake.kazutoshi/work/smallrna/matsuyama -u 2007:600 -i --rm c2997108/mirdeep2:1 'zcat input_1//3day-1.fq.gz > fastq.gunzip/3day-1.fq'
+ xargs '-d\n' -I '{}' -P 1 bash -c '{}'
++ find input_1// fastq.gunzip/ -maxdepth 1
++ grep -E '[.](fastq|fq)$'
+ for i in `find "$input_1"/ fastq.gunzip/ -maxdepth 1 |grep -E '[.](fastq|fq)$' || true`
++ basename input_1//Cont-1.fastq
++ basename input_1//Cont-1.fastq
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-smallRNA-miRDeep2/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi:/data/yoshitake.kazutoshi -v /suikou/files/m768/yoshitake.kazutoshi/work/smallrna/matsuyama:/suikou/files/m768/yoshitake.kazutoshi/work/smallrna/matsuyama -u 2007:600 -i --rm c2997108/mirdeep2:1 mapper.pl input_1//Cont-1.fastq -e -h -p input_3//pfu4A-B_birnaA-B.fa -s Cont-1.fastq.reads_collapsed.fa -t Cont-1.fastq.reads_vs_refdb.arf -i -j -k AGTCGGAGGC -l 18 -m -v -r 100 -u -n
+ for i in `find "$input_1"/ fastq.gunzip/ -maxdepth 1 |grep -E '[.](fastq|fq)$' || true`
++ basename fastq.gunzip/3day-1.fq
++ basename fastq.gunzip/3day-1.fq
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-smallRNA-miRDeep2/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi:/data/yoshitake.kazutoshi -v /suikou/files/m768/yoshitake.kazutoshi/work/smallrna/matsuyama:/suikou/files/m768/yoshitake.kazutoshi/work/smallrna/matsuyama -u 2007:600 -i --rm c2997108/mirdeep2:1 mapper.pl fastq.gunzip/3day-1.fq -e -h -p input_3//pfu4A-B_birnaA-B.fa -s 3day-1.fq.reads_collapsed.fa -t 3day-1.fq.reads_vs_refdb.arf -i -j -k AGTCGGAGGC -l 18 -m -v -r 100 -u -n
parsing fastq to fasta format
converting rna to dna alphabet
discarding sequences with non-canonical letters
clipping 3' adapters
discarding short reads
collapsing reads
mapping reads to genome index
trimming unmapped nts in the 3' ends
Log file for this run is in mapper_logs and called mapper.log_1
Mapping statistics
#desc total mapped unmapped %mapped %unmapped
total: 9052 7707 1345 85.141 14.859
seq: 9052 7707 1345 85.141 14.859
parsing fastq to fasta format
converting rna to dna alphabet
discarding sequences with non-canonical letters
clipping 3' adapters
discarding short reads
collapsing reads
mapping reads to genome index
trimming unmapped nts in the 3' ends
Log file for this run is in mapper_logs and called mapper.log_1
Mapping statistics
#desc total mapped unmapped %mapped %unmapped
total: 9088 7247 1841 79.743 20.257
seq: 9088 7247 1841 79.743 20.257
+ post_processing
+ '[' 1 = 1 ']'
+ rm -f /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-smallRNA-miRDeep2/pp-singularity-flag
+ '[' '' = y ']'
+ echo 0
+ exit