Parabricks - fq2bam "Wrong number of arguments" error

Healthcare Parabricks
#1

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

#2

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!

#3

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

#4

Hey Kostas,

I would try using -M instead of M for the bwa options, as outlined in the documentation below:

image
image935×65 2.23 KB

#5

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

#6

Hi Kostas,

can you please try --bwa-options=-M

Best

#7

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

#8

Happy to hear that!

#9

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

#10

Are you using singularity?

#11

yes

#12

To solve this error please reinstall the software using the option --disable-fakeroot .

Best
Myrieme

#13

Thanks, Myrieme. I will give it a try.

Best
Kostas