Fq2bam rel3-nanopore-wgs-288418386-FAB39088.fastq.gz

Healthcare Parabricks
1

Hi. Please help to debug.
Sample downloaded from
aws s3 cp s3://nanopore-human-wgs/rel3-nanopore-wgs-288418386-FAB39088.fastq.gz .

sudo pbrun fq2bam --ref Ref/Homo_sapiens_assembly38.fasta \
	--in-se-fq rel3-nanopore-wgs-288418386-FAB39088.fastq.gz \
	--knownSites Ref/Homo_sapiens_assembly38.known_indels.vcf.gz \
	--out-recal-file recal_gpu.txt \
	--out-bam mark_dups_gpu.bam \
	--tmp-dir /raid
Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation


[Parabricks Options Mesg]: Checking argument compatibility
[Parabricks Options Mesg]: Automatically generating ID prefix
[Parabricks Options Mesg]: Read group created for /raid/rel3-nanopore-wgs-288418386-FAB39088.fastq.gz
[Parabricks Options Mesg]:
@RG\tID:0cf3beca-6611-4690-b756-32f304.1\tLB:lib1\tPL:bar\tSM:sample\tPU:0cf3beca-6611-4690-b756-32f304.1
------------------------------------------------------------------------------
||                 Parabricks accelerated Genomics Pipeline                 ||
||                           Version v3.2.0_ampere                          ||
||                       GPU-BWA mem, Sorting Phase-I                       ||
||                  Contact: Parabricks-Support@nvidia.com                  ||
------------------------------------------------------------------------------
[M::bwa_idx_load_from_disk] read 0 ALT contigs

GPU-BWA mem
ProgressMeter	Reads		Base Pairs Aligned
PARABRICKS: ParaBricks/src/CReadWrite.cpp:197: bool FastQReader::getSingleGZRead(bseq1_t*, int, char*, int&, int&): Assertion `(sizeOfSeq < MAX_READ_SIZE) || (!printf("Size of seq is %d\n", sizeOfSeq))' failed.
Received signal: 6
Please make sure you have enough disk space in the output and temp directory
Contact Parabricks-Support@nvidia.com for support
2493: a6701b1e-67ed-4a56-8225-ad4234af3eef_Basecall_Alignment_template
Size of seq is 2493
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...

Could not run fq2bam
Exiting pbrun ...
2

Hi Alex,

We are sorry that you are facing this error.
Unfortunately, fq2bam is only intended for short reads, and here your you use a long reads fastq file.

Myrieme

3

Hi, mdemouth.

Thank you for your reply.
Another question. Originally BWA MEM works with Oxford Nanopore reads. Is this option -x implemented in Parabriks? Or Parabricks does work exclusively with Illumina?

4

I wish to report the exact same thing happens with PacBio reads when using the minimap2 from version 4.2.1 parabricks. There is a hardcoded limit of 100,000bp. If a bam contains a read that long or longer, then the entire application collapses like a house of cards and ends the alignment. It would be better if it would just skip that read or, better yet, increase the maximum read size to be larger than this. There are some reads that are better than 30kb and sometimes it happens. There should be a way to deal with it gracefully.

5

Hi @jamesdalg,

This issue will be fixed in the next version of Parabricks 4.3.

Thank you for your patience.

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