Fq2bamfast paired file error vs fq2bam Version 4.3.1-1

Healthcare & Life Sciences Parabricks
1

Hello,
I just wanted to alert to an error I get when trying to use fq2bamfast that does not appear with fq2bam:
[PB ^[[31mError^[[0m 2024-Sep-06 10:33:02][src/PBParallelFastqFile.cpp:258] paired reads have different names: “A00330:159:H3HNYDSX7:1:1101:11957:2065”, “A00330:159:H3HNYDSX7:1:1101:11595:2065” in file /mendel-nas1/ddebaun/illumina/BLUE/Ithycyphus_oursi_355_RAX9840/Ithycyphus_oursi_355_RAX9840_for_paired_clean.fq.gz and /mendel-nas1/ddebaun/illumina/BLUE/Ithycyphus_oursi_355_RAX9840/Ithycyphus_oursi_355_RAX9840_rev_paired_clean.fq.gz

I have looked into the files and they are in fact approporiately paired and these names are identical so I’m not sure why this error would appear for this fast version and not the regular one. I will stick with fq2bam

2

Hello, there are two reasons this could happen.

  1. There are actually reads in one pair of the FASTQ that don’t match up to the other (uncommon unless you’ve been modifying the FASTQs).
  2. There are two parameters that can filter the FASTQ file called --min-read-length and --max-read-length. Sometimes during pair-ended alignment only one of the two FASTQ files fails the filter so a read is filtered in one of the FASTQs but not the other. I’ve seen this happen where one of the pairs has a very small read. Try setting --min-read-length 0 explicitly so that it does not use the default of 10.

Reference to docs: fq2bamfast (BWA-MEM + GATK) - NVIDIA Docs.

3

The second option worked, thank you!

1 Like
4

Great! I’m glad your problem was solved. Your feedback was appreciated and we’ve updated our defaults to be less restrictive in v4.3.2 which just came out. Clara Parabricks v4.3.2 - NVIDIA Docs

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