Error while using pbsv discover, "ERROR: map::at"
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4 weeks ago
wch2123 ▴ 10

Hello, I am having trouble using the Pacific Biosciences tool pbsv discover. Using the Docker image from Pacific Biosciences, pacificbiosciences/pbsv, I run the command in terminal-

$ singularity exec pbsv.sif pbsv discover [input bam file] [output svsig.gz file]

but the execution fails after just a moment and prints the following error-

>|> 20240621 13:35:07.330 -|- FATAL -|- Run -|- 0x7f3c69667b80|| -|- pbsv discover ERROR: map::at

with no further information. I have tried re-indexing the bam files using samtools, but that had no effect. Below is a screenshot which includes part of one bam file header, in case there is any information in here that is useful:

screenshot from bam file header

I would try to re-align the files using the pbmm2 align tool but we receive these samples from the Broad Institute already aligned, and don't have access to the raw reads.

Any suggestions would be great, and I am able to provide more information if needed. Thanks!

bam PacBio pbsv • 344 views
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28 days ago
Billy Rowell ▴ 330

It's likely a version mismatch between pbmm2 and pbsv.

The docker images in DockerHub haven't been updated in a while. I'll try to get them removed.

There are newer images in Quay.io. Pull the image below and try it instead.

singularity pull docker://quay.io/pacbio/pbsv:2.9.0_1.14_build1
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Thanks Billy, that fixed the mapping error. Appreciate your help!

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