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kcleal / dysgu

Toolkit for calling structural variants using short or long reads
MIT License
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Paired-end reads calling sv #88

Closed C-YONG closed 3 months ago

C-YONG commented 3 months ago

When I call call SVs, there was an error dysgu run --sites combined_chang.vcf genomic.fna wd /mnt/f/rmbam/4.sort.rmdup.bam > sample1.vcf image

kcleal commented 3 months ago

Hi @C-YONG, Thanks for raising this. It is probably an issue with dysgu1.6.3. Would you be able to install v1.6.2? Could you tell me what aligner you are using?

C-YONG commented 3 months ago

Thank you for your answer, I use the 1.6.2 version, do I need to use the latest version？

C-YONG commented 3 months ago

I used the BWA alignment software for alignment, followed by using Picard to remove duplicates.

kcleal commented 3 months ago

Sorry, I've just had a look at the code that is causing this, I don't think either will solve the issue.

For some reason the name of the reference genome can't be encoded in ascii format. Are there any unusual characters in the reference genome name, the one provided on the command line? This is the problem line that is failing:

fasta_b = args["reference"].encode("ascii")
kcleal commented 3 months ago

Could you provide the full stderr output from the run? Thanks!

C-YONG commented 3 months ago

Thank you very much for your help, the cause of the error was unusual character in the name of the reference genome, we changed it and the programme works fine!