Sir,
I am getting the following error while running pbrun applybqsr on fastq files (both command line and error traceback):
Command:
pbrun applybqsr --ref /home/vivekr/refs/hg19/ucsc.hg19.fasta --in-bam /home/vivekr/bqsr/SRR2128432_mark.bam --in-recal-file /home/vivekr/bqsr/SRR2128432_recal.txt --interval-file /home/vivekr/refs/hg19/hglift_genome1.bed --out-bam /home/vivekr/bqsr/SRR2128432_bqsr.bam
Error meaasge:
Traceback (most recent call last):
File "/usr/bin/pbrun", line 14, in <module>
pbmaster.pb_main(runArgs)
File "/opt/parabricks/pbmaster.py", line 248, in pb_main
RunDNABricks(runArgs, IOMapping)
File "/opt/parabricks/pbmaster.py", line 204, in RunDNABricks
if runArgs.runArgs.gpu_devices == "all":
AttributeError: 'Namespace' object has no attribute 'gpu_devices'
Kindly suggest how to rectify this error. Thanks.
I temporarily modified the code to pass the checking.
$ sudo nano -l /opt/parabricks/pbmaster.py
Before:
if runArgs.runArgs.gpu_devices == "all":
After:
if True or runArgs.runArgs.gpu_devices == "all":
Then you can run pbrun applybqsr.
docker run --gpus all -u=1000:1000 --rm -w=/uploads2/workspace/parabricks_sample --net=host -v /opt/parabricks:/INSTALL/ -v /uploads2/workspace/parabricks_sample/TUMTQ1UJ:/uploads2/workspace/parabricks_sample/TUMTQ1UJ -v /uploads2/workspace/parabricks_sample:/uploads2/workspace/parabricks_sample -v /uploads2/workspace/parabricks_sample/Ref:/uploads2/workspace/parabricks_sample/Ref parabricks/release:v3.5.0 applybqsr --ref Ref/Homo_sapiens_assembly38.fasta --in-bam output.bam --in-recal-file report.txt --out-bam output_updated.bam --x3 --tmp-dir /uploads2/workspace/parabricks_sample/TUMTQ1UJ
Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation
/usr/local/cuda/.pb/binaries//bin/applyBQSR /uploads2/workspace/parabricks_sample/output.bam /uploads2/workspace/parabricks_sample/Ref/Homo_sapiens_assembly38.fasta /uploads2/workspace/parabricks_sample/report.txt /uploads2/workspace/parabricks_sample/output_updated.bam 1 -n 8
------------------------------------------------------------------------------
|| Parabricks accelerated Genomics Pipeline ||
|| Version v3.5.0 ||
|| applybqsr ||
|| Contact: Parabricks-Support@nvidia.com ||
------------------------------------------------------------------------------
ProgressMeter - Current-Locus Elapsed-Minutes
ProgressMeter - chr1:11114843 0.0
ProgressMeter - chr1:46033780 0.0
ProgressMeter - chr1:119415357 0.1
ProgressMeter - chr1:156912554 0.1
ProgressMeter - chr1:237678057 0.1
ProgressMeter - chr2:47419640 0.1
ProgressMeter - chr2:140716812 0.1
ProgressMeter - chr2:230310082 0.1
ProgressMeter - chr3:62203160 0.1
ProgressMeter - chr3:157150067 0.2
ProgressMeter - chr4:61732787 0.2
ProgressMeter - chr4:139060647 0.2
ProgressMeter - chr5:45049363 0.2
ProgressMeter - chr5:138319269 0.2
ProgressMeter - chr5:180629969 0.2
ProgressMeter - chr6:51523895 0.3
ProgressMeter - chr6:117341226 0.3
ProgressMeter - chr7:18648302 0.3
ProgressMeter - chr7:78125655 0.3
ProgressMeter - chr7:116759236 0.3
ProgressMeter - chr7:152250864 0.3
ProgressMeter - chr8:41749734 0.4
ProgressMeter - chr8:89955347 0.4
ProgressMeter - chr9:4118911 0.4
ProgressMeter - chr9:42248904 0.4
ProgressMeter - chr9:108220920 0.4
ProgressMeter - chr10:6021438 0.5
ProgressMeter - chr10:68681182 0.5
ProgressMeter - chr10:99843608 0.5
ProgressMeter - chr11:8242439 0.5
ProgressMeter - chr11:63032731 0.5
ProgressMeter - chr11:108282697 0.5
ProgressMeter - chr12:40259365 0.6
ProgressMeter - chr12:116461225 0.6
ProgressMeter - chr13:75855386 0.6
ProgressMeter - chr14:69637281 0.6
ProgressMeter - chr15:67826566 0.6
ProgressMeter - chr16:28726542 0.6
ProgressMeter - chr17:5380513 0.7
ProgressMeter - chr17:42722931 0.7
ProgressMeter - chr18:2706419 0.7
ProgressMeter - chr19:6842902 0.7
ProgressMeter - chr19:48981845 0.7
ProgressMeter - chr21:10569393 0.7
ProgressMeter - chr22:50248037 0.8
ProgressMeter - chrX:150470299 0.8
ProgressMeter - Unmapped:0 0.8
------------------------------------------------------------------------------
|| Program: applybqsr ||
|| Version: v3.5.0 ||
|| Start Time: Thu Jul 8 16:48:41 2021 ||
|| End Time: Thu Jul 8 16:49:30 2021 ||
|| Total Time: 49 seconds ||
------------------------------------------------------------------------------
Time 48.177(564.916) seconds
Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation