mapping-illumina~parabricks

NVIDIA Parabricks mapping tool. This tool needs NVIDIA GPU with over 16GB GPU memory.

input_1:paired-end FASTQ or single FASTQ(.gz) files

input_1/SRR1363434_10k_1.fastq

@SRR1363434.1 HWI-ST615:215:C0MJTACXX:2:1101:1323:2406 length=101
ATTCTTGCCAGCCTGGAACTTCTTCCTTCATACCGTGTCTCTTACGAGCAGCAAGAACAATTTCACCAGCCTTAGAGGTTGGGTCCAATGGGTCAGAACCT
+SRR1363434.1 HWI-ST615:215:C0MJTACXX:2:1101:1323:2406 length=101
CC@FFFFFHGHHHIJGIJJJJHJJJJJIJJJJJGIIGIJIJIJJJIGGIGJJJJIHIIFIJIJJJJJFFHHFDFCDDDEEEDDBDBDDDCDDACDCDDCA9
@SRR1363434.2 HWI-ST615:215:C0MJTACXX:2:1101:1379:2415 length=101
TTTCGTTCTTGATTAATGAAAACGTCCTTGGCAAATGCTTTCGCAGTAGTTAGTCTTCAATAAATCCAAGAATTTCACCTCTGACAATTGAATACTGATGC
+SRR1363434.2 HWI-ST615:215:C0MJTACXX:2:1101:1379:2415 length=101
CCCFFFFFHGHHHJJJJJJJJJJJEHIJJJJJJJJJJJJJJJJJJIGHIIIGJIJJIJIIIJIGIJJJJJJHHHHFHHDFFFFCEEEDDCCCDEDDEDCCC
@SRR1363434.3 HWI-ST615:215:C0MJTACXX:2:1101:1298:2472 length=101
CGCCAGTGCTCCAGTTGTTACCTGAGAATGAAGCTTGATCGGCTTTTATTCTTTCCTGATAGGACTCTGTAAGTGTTACTAAACACTAACCGGTGAAGGAA

input_1/SRR1363434_10k_2.fastq

@SRR1363434.1 HWI-ST615:215:C0MJTACXX:2:1101:1323:2406 length=101
GTCGTTTCTGAAGAACAAAGACCAGGTACTCCATTGTTTACCGTCAAGGCCTACTTGCCAGTTAACGAATCTTTCGGTTTCACTGGTGAATTGAGACAAGC
+SRR1363434.1 HWI-ST615:215:C0MJTACXX:2:1101:1323:2406 length=101
@@BFFFFFHHHHHJJJJJJJJJJIJJFHHIIJIJJJIIIIHIJHGIIJIJGIGIJIJJJGIFGGJJJHEFHCFFFFDCC@CDDCDBCCCCDED@CACCCBB
@SRR1363434.2 HWI-ST615:215:C0MJTACXX:2:1101:1379:2415 length=101
CTTCTGGCTAACCTTGAGTCCTTGTGGCTCTTGGCGAACCAGGACTTTTACTTTGAAAAAATTAGAGTGTTCAAAGCAGGCGTATTGCTCGAATATATTAG
+SRR1363434.2 HWI-ST615:215:C0MJTACXX:2:1101:1379:2415 length=101
CCCFFFFFHHHGHJJJIJIIIJJJHIJIJJGIEIGIDGHIIIJFFHIJJJJHHJIHIJJJHFFFFFF>CCFEEECCDCDD?B?BDDDDCD@9CCDEEEEDE
@SRR1363434.3 HWI-ST615:215:C0MJTACXX:2:1101:1298:2472 length=101
GTAGTAATGGTTTCAAGGGTTATCGATCACAGACATCATTGGTACGATGTTGTCTCTGGAGCTGTTCTAGCATTTTTAGTCATTTATTGTTGCTGGAAATG

input_2:reference genome file

input_2/ref.fasta

>chrI
CCACACCACACCCACACACCCACACACCACACCACACACCACACCACACCCACACACACA
CATCCTAACACTACCCTAACACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTT
ACCCTCCATTACCCTGCCTCCACTCGTTACCCTGTCCCATTCAACCATACCACTCCGAAC
CACCATCCATCCCTCTACTTACTACCACTCACCCACCGTTACCCTCCAATTACCCATATC
CAACCCACTGCCACTTACCCTACCATTACCCTACCATCCACCATGACCTACTCACCATAC
TGTTCTTCTACCCACCATATTGAAACGCTAACAAATGATCGTAAATAACACACACGTGCT
TACCCTACCACTTTATACCACCACCACATGCCATACTCACCCTCACTTGTATACTGATTT
TACGTACGCACACGGATGCTACAGTATATACCATCTCAAACTTACCCTACTCTCAGATTC
CACTTCACTCCATGGCCCATCTCTCACTGAATCAGTACCAAATGCACTCACATCATTATG

input_3:bwa index

Command

mapping-illumina~parabricks -c 8 -m 32 input_1/ input_2/ref.fasta

Output

output.parabricks.bam

view all outputs

Log

pp mapping-illumina~parabricks -c 8 -m 32 input_1/ input_2/ref.fasta
PID: 97921
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/pp 'mapping-illumina~parabricks' -c 8 -m 32 input_1/ input_2/ref.fasta
Checking the realpath of input files.
0 input_1/
1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks/input_1/SRR1363434_10k_1.fastq
1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks/input_1/SRR1363434_10k_2.fastq
0 input_2/ref.fasta
0
/home/yoshitake.kazutoshi/work -> /data/yoshitake.kazutoshi/work
/home/yoshitake.kazutoshi/work/pp-dev -> /data/yoshitake.kazutoshi/work/pp-dev
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks
/data/yoshitake.kazutoshi/work
/data/yoshitake.kazutoshi/work/pp-dev
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks
biocontainers/samtools:v1.7.0_cv4 centos:centos6 nvcr.io/nvidia/clara/clara-parabricks:4.1.0-1 quay.io/biocontainers/bwa:0.7.17--pl5.22.0_1
using docker
+ set -o pipefail
+ '[' '' = '' ']'
+ FUNC_RUN_DOCKER quay.io/biocontainers/bwa:0.7.17--pl5.22.0_1 bwa index input_2/ref.fasta
+ PP_RUN_IMAGE=quay.io/biocontainers/bwa:0.7.17--pl5.22.0_1
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20240116_222847_739_20588
+ echo pp20240116_222847_739_20588
++ id -u
++ id -g
+ docker run --name pp20240116_222847_739_20588 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks -u 2007:600 -i --rm quay.io/biocontainers/bwa:0.7.17--pl5.22.0_1 bwa index input_2/ref.fasta
[bwa_index] Pack FASTA... 0.12 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 4.04 seconds elapse.
[bwa_index] Update BWT... 0.07 sec
[bwa_index] Pack forward-only FASTA... 0.05 sec
[bwa_index] Construct SA from BWT and Occ... 1.64 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index input_2/ref.fasta
[main] Real time: 6.318 sec; CPU: 5.967 sec
+ ref=input_2/ref.fasta
+ mkdir -p output.bwa
++ ls input_1//
++ grep -E '[.]f(ast|)q(|[.]gz)$'
++ awk '
{file[$0]=1}
END{ORS=" "
for(i in file){
if(flag[i]!=1){
r1=i;
r2="";
if(i~"_1[.]f(ast|)q(|[.]gz)$"){
flag[i]=1;
samplename=gensub(/_1[.]f(ast|)q(|[.]gz)$/,"",1,i);
j=gensub(/_1[.]f(ast|)q(|[.]gz)$/,"_2.f\1q\2",1,i);
if(j in file){
flag[j]=1;
r2=j;
}
}else if(i~"_R1(.*)[.]f(ast|)q(|[.]gz)$"){
flag[i]=1;
samplename=gensub(/_R1(.*)[.]f(ast|)q(|[.]gz)$/,"",1,i);
j=gensub(/_R1(.*)[.]f(ast|)q(|[.]gz)$/,"_R2\1.f\2q\3",1,i);
if(j in file){
flag[j]=1;
r2=j;
}
}
if(flag[i]==1){
print "--in-fq "r1" "r2
}
}
}
for(i in file){
if(flag[i]!=1){
r1=i;
samplename=gensub(/[.]f(ast|)q(|[.]gz)$/,"",1,i);
flag[i]=1;
print "--in-se-fq "r1
}
}
}
'
+ reads='--in-fq SRR1363434_10k_1.fastq  --in-se-fq SRR1363434_10k_2.fastq '
+ FUNC_RUN_DOCKER_GPU nvcr.io/nvidia/clara/clara-parabricks:4.1.0-1 pbrun fq2bam --ref input_2/ref.fasta --in-fq SRR1363434_10k_1.fastq --in-se-fq SRR1363434_10k_2.fastq --out-bam output.parabricks.bam --no-markdups
+ PP_RUN_IMAGE=nvcr.io/nvidia/clara/clara-parabricks:4.1.0-1
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20240116_222854_840_6086
+ echo pp20240116_222854_840_6086
++ id -u
++ id -g
+ docker run --name pp20240116_222854_840_6086 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks -u 2007:600 -i --rm --gpus all nvcr.io/nvidia/clara/clara-parabricks:4.1.0-1 pbrun fq2bam --ref input_2/ref.fasta --in-fq SRR1363434_10k_1.fastq --in-se-fq SRR1363434_10k_2.fastq --out-bam output.parabricks.bam --no-markdups
Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation


[Parabricks Options Error]: Input file SRR1363434_10k_1.fastq not found. Exiting...
[Parabricks Options Error]: Run with -h to see help

PID: 120673
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/pp 'mapping-illumina~parabricks' -c 8 -m 32 input_1/ input_2/ref.fasta
Checking the realpath of input files.
0 input_1/
1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks/input_1/SRR1363434_10k_1.fastq
1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks/input_1/SRR1363434_10k_2.fastq
0 input_2/ref.fasta
0
/home/yoshitake.kazutoshi/work -> /data/yoshitake.kazutoshi/work
/home/yoshitake.kazutoshi/work/pp-dev -> /data/yoshitake.kazutoshi/work/pp-dev
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks
/data/yoshitake.kazutoshi/work
/data/yoshitake.kazutoshi/work/pp-dev
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks
biocontainers/samtools:v1.7.0_cv4 centos:centos6 nvcr.io/nvidia/clara/clara-parabricks:4.1.0-1 quay.io/biocontainers/bwa:0.7.17--pl5.22.0_1
using docker
+ set -o pipefail
+ '[' '' = '' ']'
+ FUNC_RUN_DOCKER quay.io/biocontainers/bwa:0.7.17--pl5.22.0_1 bwa index input_2/ref.fasta
+ PP_RUN_IMAGE=quay.io/biocontainers/bwa:0.7.17--pl5.22.0_1
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20240116_225148_763_1365
+ echo pp20240116_225148_763_1365
++ id -u
++ id -g
+ docker run --name pp20240116_225148_763_1365 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks -u 2007:600 -i --rm quay.io/biocontainers/bwa:0.7.17--pl5.22.0_1 bwa index input_2/ref.fasta
[bwa_index] Pack FASTA... 0.10 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 3.92 seconds elapse.
[bwa_index] Update BWT... 0.08 sec
[bwa_index] Pack forward-only FASTA... 0.06 sec
[bwa_index] Construct SA from BWT and Occ... 1.49 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index input_2/ref.fasta
[main] Real time: 5.941 sec; CPU: 5.698 sec
+ ref=input_2/ref.fasta
+ mkdir -p output.bwa
++ ls input_1//
++ grep -E '[.]f(ast|)q(|[.]gz)$'
++ awk '
{file[$0]=1}
END{
ORS=" "
PROCINFO["sorted_in"]="@ind_str_asc"
for(i in file){
if(flag[i]!=1){
r1=i;
r2="";
if(i~"_1[.]f(ast|)q(|[.]gz)$"){
flag[i]=1;
samplename=gensub(/_1[.]f(ast|)q(|[.]gz)$/,"",1,i);
j=gensub(/_1[.]f(ast|)q(|[.]gz)$/,"_2.f\\1q\\2",1,i);
if(j in file){
flag[j]=1;
r2=j;
}
}else if(i~"_R1(.*)[.]f(ast|)q(|[.]gz)$"){
flag[i]=1;
samplename=gensub(/_R1(.*)[.]f(ast|)q(|[.]gz)$/,"",1,i);
j=gensub(/_R1(.*)[.]f(ast|)q(|[.]gz)$/,"_R2\\1.f\\2q\\3",1,i);
if(j in file){
flag[j]=1;
r2=j;
}
}
if(flag[r2]==1){
print "--in-fq "r1" "r2
}else{
flag[r1]=0
}
}
}
for(i in file){
if(flag[i]!=1){
r1=i;
samplename=gensub(/[.]f(ast|)q(|[.]gz)$/,"",1,i);
flag[i]=1;
print "--in-se-fq "r1
}
}
}
'
+ reads='--in-fq SRR1363434_10k_1.fastq SRR1363434_10k_2.fastq '
+ FUNC_RUN_DOCKER_GPU nvcr.io/nvidia/clara/clara-parabricks:4.1.0-1 pbrun fq2bam --ref input_2/ref.fasta --in-fq SRR1363434_10k_1.fastq SRR1363434_10k_2.fastq --out-bam output.parabricks.bam --no-markdups
+ PP_RUN_IMAGE=nvcr.io/nvidia/clara/clara-parabricks:4.1.0-1
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20240116_225155_536_8141
+ echo pp20240116_225155_536_8141
++ id -u
++ id -g
+ docker run --name pp20240116_225155_536_8141 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks -u 2007:600 -i --rm --gpus all nvcr.io/nvidia/clara/clara-parabricks:4.1.0-1 pbrun fq2bam --ref input_2/ref.fasta --in-fq SRR1363434_10k_1.fastq SRR1363434_10k_2.fastq --out-bam output.parabricks.bam --no-markdups
Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation


[Parabricks Options Error]: Input file SRR1363434_10k_1.fastq not found. Exiting...
[Parabricks Options Error]: Run with -h to see help

PID: 122894
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/pp 'mapping-illumina~parabricks' -c 8 -m 32 input_1/ input_2/ref.fasta
Checking the realpath of input files.
0 input_1/
1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks/input_1/SRR1363434_10k_1.fastq
1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks/input_1/SRR1363434_10k_2.fastq
0 input_2/ref.fasta
0
/home/yoshitake.kazutoshi/work -> /data/yoshitake.kazutoshi/work
/home/yoshitake.kazutoshi/work/pp-dev -> /data/yoshitake.kazutoshi/work/pp-dev
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks
/data/yoshitake.kazutoshi/work
/data/yoshitake.kazutoshi/work/pp-dev
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks
biocontainers/samtools:v1.7.0_cv4 centos:centos6 nvcr.io/nvidia/clara/clara-parabricks:4.1.0-1 quay.io/biocontainers/bwa:0.7.17--pl5.22.0_1
using docker
+ set -o pipefail
+ '[' '' = '' ']'
+ FUNC_RUN_DOCKER quay.io/biocontainers/bwa:0.7.17--pl5.22.0_1 bwa index input_2/ref.fasta
+ PP_RUN_IMAGE=quay.io/biocontainers/bwa:0.7.17--pl5.22.0_1
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20240116_225344_035_16278
+ echo pp20240116_225344_035_16278
++ id -u
++ id -g
+ docker run --name pp20240116_225344_035_16278 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks -u 2007:600 -i --rm quay.io/biocontainers/bwa:0.7.17--pl5.22.0_1 bwa index input_2/ref.fasta
[bwa_index] Pack FASTA... 0.11 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 4.03 seconds elapse.
[bwa_index] Update BWT... 0.05 sec
[bwa_index] Pack forward-only FASTA... 0.05 sec
[bwa_index] Construct SA from BWT and Occ... 1.53 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index input_2/ref.fasta
[main] Real time: 6.000 sec; CPU: 5.820 sec
+ ref=input_2/ref.fasta
+ mkdir -p output.bwa
++ ls input_1//
++ grep -E '[.]f(ast|)q(|[.]gz)$'
++ awk -v input_1=input_1/ '
{file[$0]=1}
END{
ORS=" "
PROCINFO["sorted_in"]="@ind_str_asc"
for(i in file){
if(flag[i]!=1){
r1=i;
r2="";
if(i~"_1[.]f(ast|)q(|[.]gz)$"){
flag[i]=1;
samplename=gensub(/_1[.]f(ast|)q(|[.]gz)$/,"",1,i);
j=gensub(/_1[.]f(ast|)q(|[.]gz)$/,"_2.f\\1q\\2",1,i);
if(j in file){
flag[j]=1;
r2=j;
}
}else if(i~"_R1(.*)[.]f(ast|)q(|[.]gz)$"){
flag[i]=1;
samplename=gensub(/_R1(.*)[.]f(ast|)q(|[.]gz)$/,"",1,i);
j=gensub(/_R1(.*)[.]f(ast|)q(|[.]gz)$/,"_R2\\1.f\\2q\\3",1,i);
if(j in file){
flag[j]=1;
r2=j;
}
}
if(flag[r2]==1){
print "--in-fq "input_1"/"r1" "input_1"/"r2
}else{
flag[r1]=0
}
}
}
for(i in file){
if(flag[i]!=1){
r1=i;
samplename=gensub(/[.]f(ast|)q(|[.]gz)$/,"",1,i);
flag[i]=1;
print "--in-se-fq "input_1"/"r1
}
}
}
'
+ reads='--in-fq input_1//SRR1363434_10k_1.fastq input_1//SRR1363434_10k_2.fastq '
+ FUNC_RUN_DOCKER_GPU nvcr.io/nvidia/clara/clara-parabricks:4.1.0-1 pbrun fq2bam --ref input_2/ref.fasta --in-fq input_1//SRR1363434_10k_1.fastq input_1//SRR1363434_10k_2.fastq --out-bam output.parabricks.bam --no-markdups
+ PP_RUN_IMAGE=nvcr.io/nvidia/clara/clara-parabricks:4.1.0-1
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20240116_225350_898_31786
+ echo pp20240116_225350_898_31786
++ id -u
++ id -g
+ docker run --name pp20240116_225350_898_31786 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-illumina~parabricks -u 2007:600 -i --rm --gpus all nvcr.io/nvidia/clara/clara-parabricks:4.1.0-1 pbrun fq2bam --ref input_2/ref.fasta --in-fq input_1//SRR1363434_10k_1.fastq input_1//SRR1363434_10k_2.fastq --out-bam output.parabricks.bam --no-markdups

[Parabricks Options Mesg]: Checking argument compatibility
[Parabricks Options Mesg]: Automatically generating ID prefix
[Parabricks Options Mesg]: Read group created for /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-
illumina~parabricks/input_1/SRR1363434_10k_1.fastq and /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/mapping-
illumina~parabricks/input_1/SRR1363434_10k_2.fastq
[Parabricks Options Mesg]: @RG\tID:SRR1363434.1.1\tLB:lib1\tPL:bar\tSM:sample\tPU:SRR1363434.1.1
[PB Info 2024-Jan-16 13:53:54] ------------------------------------------------------------------------------
[PB Info 2024-Jan-16 13:53:54] ||                 Parabricks accelerated Genomics Pipeline                 ||
[PB Info 2024-Jan-16 13:53:54] ||                              Version 4.1.0-1                             ||
[PB Info 2024-Jan-16 13:53:54] ||                       GPU-BWA mem, Sorting Phase-I                       ||
[PB Info 2024-Jan-16 13:53:54] ------------------------------------------------------------------------------
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[PB Info 2024-Jan-16 13:53:55] GPU-BWA mem
[PB Info 2024-Jan-16 13:53:55] ProgressMeter	Reads		Base Pairs Aligned
[PB Warning 2024-Jan-16 13:53:57][ParaBricks/src/check_error.cu:41] cudaSafeCall() failed at ParaBricks/src/samGenerator.cu/772: out of memory
[PB Error 2024-Jan-16 13:53:57][ParaBricks/src/check_error.cu:44] No GPUs active, shutting down due to previous error., exiting.
For technical support visit https://docs.nvidia.com/clara/parabricks/4.1.0/Help.html
Exiting...
Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation



Could not run fq2bam
Exiting pbrun ...