Fq2bam: Unexpected Issue #1, Return code: 2

Hi, I was trying to use the command fq2bam, follows the command line:

singularity exec --nv --bind /archive/s1/data_energon/:/media/,/hpcshare/genomics/references/gatk_bundle/:/mnt ./pipelines/parabricks/parabricks-release-v3.2.0.sif
/parabricks/run_pipeline.py fq2bam --x1 --x3
–ref /mnt/reference/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta
–in-fq /media/181119_A00558_0012_BHF5V5DSXX/10643_06_KID_S6_R1_001.fastq.gz /media/181119_A00558_0012_BHF5V5DSXX/10643_06_KID_S6_R2_001.fastq.gz
–knownSites /mnt/resources/resources_broad_hg38_v0_hapmap_3.3.hg38.vcf.gz
–out-bam /homenfs/smarangoni/out_gpu.bam
–out-recal-file recal_gpu.txt
–license-file ./pipelines/parabricks/license.bin

And the programm returned:

Please visit NVIDIA Clara Documentation for detailed documentation

[Parabricks Options Mesg]: Checking argument compatibility
[Parabricks Options Mesg]: Automatically generating ID prefix
[Parabricks Options Mesg]: Read group created for /media/181119_A00558_0012_BHF5V5DSXX/10643_06_KID_S6_R1_001.fastq.gz
and /media/181119_A00558_0012_BHF5V5DSXX/10643_06_KID_S6_R2_001.fastq.gz
[Parabricks Options Mesg]: @RG\tID:HF5V5DSXX.1\tLB:lib1\tPL:bar\tSM:sample\tPU:HF5V5DSXX.1
Unexpected Issue #1, Return code: 2
Please contact Parabricks-Support@nvidia.com for any questions
There is a forum for Q&A as well at https://forums.developer.nvidia.com/c/healthcare/Parabricks/290
Exiting…

So I ask, what type of error is “Unexpected Issue #1, Return code: 2”

Thanks in advice

Hi,
I am having the same problem and cannot understand where the error is coming from.
The only difference is that I am running a full pipeline using NVIDIA test samples as input:


pbrun germline --ref Homo_sapiens_assembly38.fasta \\ 
                         --in-fq sample1_1.fq.gz  sample1_2.fq.gz \\
			 --knownSites Homo_sapiens_assembly38.known_indels.vcf.gz \\
			 --out-bam output_parabricks.bam \\
			 --out-variants output_parabricks.vcf \\
			 --out-recal-file report_parabricks.txt \

Did you receive any sort of support on this?
Thanks!

Hi, in the end I resolved my problem, using the command “pbrun” instead using the singularity container. Have you tried using the “–x1” and “–x3” in order to increase the verbosity? Are the error text the same I posted ? In case it is different, can you post the text of the error so I can understand ?

I just ran pbrun fq2bam using –x1 --x3. The run uses 2 GPUs by default. I include the last part of the output as the first part finished without any error:

Total GPUs time: 127.375602 seconds


Total IO Reader Processing time: 127.375610 seconds


Total IO Writer Processing time: 130.307173 seconds


GPU-BWA Mem time: 130.307189 seconds
GPU-BWA Mem is finished.

GPU Sorting, Marking Dups, BQSR
ProgressMeter	SAM Entries Completed
ChunkQueue Final report: Out of 614 chunks 0 failed: 0.000000% failure

PE Statistics
0, 0
1, 0

Destroying time: 0.001763 seconds



Total GPU-BWA Mem + Sorting + MarkingDups + BQSR Generation + BAM writing
Processing time: 146.478868 seconds

[main] CMD: PARABRICKS mem -Z ./pbOpts.txt /fast/external/cazzaniga/references/human/broad/Homo_sapiens_assembly38.fasta /fast/external/fbarone/variant_benchmark/samples/s1_1.fq.gz /fast/external/fbarone/variant_benchmark/samples/s1_2.fq.gz @RG\tID:HK3TJBCX2.1\tLB:lib1\tPL:bar\tSM:sample\tPU:HK3TJBCX2.1
[main] Real time: 150.911 sec; CPU: 2194.010 sec
------------------------------------------------------------------------------
||        Program:                      GPU-BWA mem, Sorting Phase-I        ||
||        Version:                                            v3.1.7        ||
||        Start Time:                       Fri Feb 12 09:59:43 2021        ||
||        End Time:                         Fri Feb 12 10:02:16 2021        ||
||        Total Time:                           2 minutes 33 seconds        ||
------------------------------------------------------------------------------
/parabricks/sort -sort_unmapped -ft 10 -gb 125 -v
------------------------------------------------------------------------------
||                 Parabricks accelerated Genomics Pipeline                 ||
||                              Version v3.1.7                              ||
||                             Sorting Phase-II                             ||
||                  Contact: Parabricks-Support@nvidia.com                  ||
------------------------------------------------------------------------------
progressMeter - Percentage
Queues Task 0  Write 0
[10:02:18]	0.0	 0.00 GB
bin 9 done
bin 15 done
bin 12 done
bin 6 done
[ ... ]
bin 1009 done
bin 998 done
bin 1010 done
bin 1012 done
0.494 1.728 0.851 1.232 0.000
0.523 1.525 1.127 1.130 0.000
bin 969 done
0.534 1.289 1.301 1.180 0.000
bin 1016 done
bin 1014 done
bin 1011 done
bin 1015 done
0.595 1.594 1.042 1.074 0.000
bin 1013 done
0.684 1.515 1.016 1.091 0.000
bin 961 done
0.611 1.655 1.009 1.033 0.000
bin 999 done
0.587 1.394 1.245 1.084 0.000
bin 997 done
0.619 1.735 0.925 1.032 0.000
bin 962 done
0.609 1.838 0.843 1.023 0.000
bin 915 done
0.512 1.686 0.700 1.423 0.000
bin 946 done
Sorting and Marking: 10.000 seconds
------------------------------------------------------------------------------
||        Program:                                  Sorting Phase-II        ||
||        Version:                                            v3.1.7        ||
||        Start Time:                       Fri Feb 12 10:02:18 2021        ||
||        End Time:                         Fri Feb 12 10:02:28 2021        ||
||        Total Time:                                     10 seconds        ||
------------------------------------------------------------------------------
Unexpected Issue #1, Return code: 2
Please contact Parabricks-Support@nvidia.com for any questions. Exiting...

Could not run fq2bam
Exiting pbrun ...

Maybe it is a problem when writing the bam file? I still have no clue…

I didn’t find the source of the problem but reinstalling parabricks solved it.