thread 'main' panicked at 'assertion failed: p <= 0.0'

[menickname]

I am currently using longshot for variant calling in a reference-based bacterial genome assembly pipeline. For most genomes longshot does not render issues. However for some genomes I encounter the following error:

thread 'main' panicked at 'assertion failed: p <= 0.0'

I am using ONT reads and have set the -P 0.01 value which does not lead to a solution in this case.

Thank you in advance.
Beste regards,
Nick Vereecke

[philres]

Hi,

I get the same error with a human dataset.

Would appreciate any help.

Thanks,
Philipp

[vibansal]

Can you share a small dataset that can reproduce this error?

[menickname]

Dear @vibansal
When using long-read sequencing data (Nanopore) from viral origin, no problems occur upon implementation of longshot in the pipeline, nevertheless upon using it in a bigger dataset from bacterial origin, the error occurs. I got it again for a new dataset from another bacterial species. When using the complete dataset I got the error. This is an example of a few reads used in this analysis:
subsample_data.fastq.zip

Unfortunately, I am not able to share the complete dataset on here.
Thanks,
Nick

[SegoleneDiry]

Hi,

I get the same error on a bacterial dataset using Longshot v4.0.1
Did you fix the issue?

Thanks,

[menickname]

Dear @SegoleneDiry

I am still waiting on a respons on my final answer on July 29.
Any update on this @vibansal

Thank you in advance.

[vibansal]

If either of you can share a dataset (bam file and reference fasta) to reproduce this error, I would really like to fix it. You can upload the files to a secure OneDrive folder here

[amandawarr]

I have the same problem with a virus.

I can upload data. I've got one dataset that it will run on and one that it won't for the same reference.

[vibansal]

Thanks.

[vibansal]

Fixed. If you still encounter the error, please let us know.