Hi,
After launching fq2bam with the following command:
pbrun fq2bam
–ref /projects/020-Aubergine-SNPdiscovery/Solanum_melongena_consortium/assembly/V3/Eggplant_V3_Chromosomes_plusChr0.fa
–in-fq paired/B1303_1.fq.gz paired/B1303_2.fq.gz
–out-bam paired/BWA_output/B1303.sort.pcr_rem.RG.bam
–bwa-options M
–read-group-sm B1303
–read-group-lb 1
–read-group-pl illumina
–read-group-id-prefix B1303
–tmp-dir paired/BWA_output/
this is the output that I getting, where the last line contains the error.
indent preformatted text by 4 spaces
[Parabricks Options Mesg]: Checking argument compatibility
[Parabricks Options Mesg]: Read group created for /scratch/020-Aubergine-SNPdiscovery/PI388846_B1303-25/B1303_1.fq.gz
and /scratch/020-Aubergine-SNPdiscovery/PI388846_B1303-25/B1303_2.fq.gz
[Parabricks Options Mesg]: @RG\tID:B1303.1\tLB:1\tPL:illumina\tSM:B1303\tPU:B1303.1
------------------------------------------------------------------------------
|| Parabricks accelerated Genomics Pipeline ||
|| Version v3.1.6 ||
|| GPU-BWA mem, Sorting Phase-I ||
|| Contact: Parabricks-Support@nvidia.com ||
------------------------------------------------------------------------------
[M::bwa_idx_load_from_disk] read 0 ALT contigs
Wrong number of arguments 6 8
Any help would be appreciated!
Thanks
Kostas
Hey @alexiou5177,
Can you run the command again, but add flags --x1 and --x3? This will (hopefully) give us some more verbose output to debug with.
Thank you!
Hi @gburnett,
Thanks for your quick reply. I have included the --x1 --x3 tags and below you have the output. Note: is the format of the value of --bwa-options I am using, correct? At the help menu, you are mentioning that the accepted values are -M, -Y and -T. I have used the first option but as “M” and not as “-M” since it was the only one working. I am mentioning this just in case I am doing a stupid error and this generates downstream problems.
singularity run --nv -B /opt/rh7/parabricks-20201117/parabricks:/INSTALL/ -B /scratch/020-Aubergine-SNPdiscovery/PI388846_B1303-25/paired/BWA_output/LWIB47PA:/scratch/020-Aubergine-SNPdiscovery/PI388846_B1303-25/paired/BWA_output/LWIB47PA -B /scratch/020-Aubergine-SNPdiscovery/PI388846_B1303-25:/scratch/020-Aubergine-SNPdiscovery/PI388846_B1303-25 -B /projects/020-Aubergine-SNPdiscovery/Solanum_melongena_consortium/assembly/V3:/projects/020-Aubergine-SNPdiscovery/Solanum_melongena_consortium/assembly/V3 -B /scratch/020-Aubergine-SNPdiscovery/PI388846_B1303-25/paired/BWA_output:/scratch/020-Aubergine-SNPdiscovery/PI388846_B1303-25/paired/BWA_output --overlay /opt/rh7/parabricks-20201117/parabricks/pb-overlay.img /opt/rh7/parabricks-20201117/parabricks/parabricks-release-v3.1.6.sif fq2bam --x1 --x3 --ref /projects/020-Aubergine-SNPdiscovery/Solanum_melongena_consortium/assembly/V3/Eggplant_V3_Chromosomes_plusChr0.fa --in-fq paired/B1303_1.fq.gz paired/B1303_2.fq.gz --out-bam paired/BWA_output/B1303.sort.pcr_rem.RG.bam --bwa-options M --read-group-sm B1303 --read-group-lb 1 --read-group-pl illumina --read-group-id-prefix B1303 --tmp-dir /scratch/020-Aubergine-SNPdiscovery/PI388846_B1303-25/paired/BWA_output/LWIB47PA
Please visit https://www.nvidia.com/en-us/docs/parabricks/ for detailed documentation
[Parabricks Options Mesg]: Checking argument compatibility
[Parabricks Options Mesg]: Read group created for /scratch/020-Aubergine-SNPdiscovery/PI388846_B1303-25/B1303_1.fq.gz
and /scratch/020-Aubergine-SNPdiscovery/PI388846_B1303-25/B1303_2.fq.gz
[Parabricks Options Mesg]: @RG\tID:B1303.1\tLB:1\tPL:illumina\tSM:B1303\tPU:B1303.1
g 1 b 0 B 1 P 4 s 1 r 0 o 2 m 1 z 4 f 2 v 1 M 2 name /scratch/020-Aubergine-SNPdiscovery/PI388846_B1303-25/paired/BWA_output/B1303.sort.pcr_rem.RG.bam
/parabricks/bwa mem /projects/020-Aubergine-SNPdiscovery/Solanum_melongena_consortium/assembly/V3/Eggplant_V3_Chromosomes_plusChr0.fa /scratch/020-Aubergine-SNPdiscovery/PI388846_B1303-25/B1303_1.fq.gz /scratch/020-Aubergine-SNPdiscovery/PI388846_B1303-25/B1303_2.fq.gz @RG\tID:B1303.1\tLB:1\tPL:illumina\tSM:B1303\tPU:B1303.1 -Z ./pbOpts.txt M
------------------------------------------------------------------------------
|| Parabricks accelerated Genomics Pipeline ||
|| Version v3.1.6 ||
|| GPU-BWA mem, Sorting Phase-I ||
|| Contact: Parabricks-Support@nvidia.com ||
------------------------------------------------------------------------------
[M::bwa_idx_load_from_disk] read 0 ALT contigs
Wrong number of arguments 6 8
------------------------------------------------------------------------------
|| Program: GPU-BWA mem, Sorting Phase-I ||
|| Version: v3.1.6 ||
|| Start Time: Mon Nov 30 22:59:17 2020 ||
|| End Time: Mon Nov 30 22:59:18 2020 ||
|| Total Time: 1 second ||
------------------------------------------------------------------------------
Please contact Parabricks-Support@nvidia.com for any questions. Exiting...
Could not run fq2bam
Exiting pbrun ...
Kostas
Hey Kostas,
I would try using -M instead of M for the bwa options, as outlined in the documentation below:
Hi @gburnett,
Using either --bwa-options -M or --bwa-options '-M' gives an error of a missing argument for --bwa-options
pbrun: error: argument --bwa-options: expected one argument
command:
pbrun fq2bam --x1 --x3 --ref /projects/020-Aubergine-SNPdiscovery/Solanum_melongena_consortium/assembly/V3/Eggplant_V3_Chromosomes_plusChr0.fa --in-fq paired/B1303_1.fq.gz paired/B1303_2.fq.gz --out-bam paired/BWA_output/B1303.sort.pcr_rem.RG.bam --bwa-options -M --read-group-sm B1303 --read-group-lb 1 --read-group-pl illumina --read-group-id-prefix B1303 --tmp-dir paired/BWA_output/
Kostas
Hi Kostas,
can you please try --bwa-options=-M
Best
It’s working!!
Maybe it will be useful for the users to add this detail about the format in the help section.
Thanks a lot,
Kostas
Hi @gburnett,
One last question related to fq2bam. When I try to launch the tool on the same cluster node for another sample, I get the following error:
FATAL: while loading overlay images: failed to open overlay image /opt/rh7/parabricks-20201117/parabricks/pb-overlay.img: while locking ext3 partition from /opt/rh7/parabricks-20201117/parabricks/pb-overlay.img: can’t open /opt/rh7/parabricks-20201117/parabricks/pb-overlay.img for writing, currently in use by another process
Any ideas as a workaround for running multiple samples?
Thanks,
Kostas
Are you using singularity?
To solve this error please reinstall the software using the option --disable-fakeroot .
Best
Myrieme
Thanks, Myrieme. I will give it a try.
Best
Kostas
