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nf-core / bacass

Simple bacterial assembly and annotation pipeline
https://nf-co.re/bacass
MIT License
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Bakta running only for one sample #171

Closed SchwarzMarek closed 1 month ago

SchwarzMarek commented 1 month ago

Description of the bug

When running bacass for multiple samples, bakta output is produced only for one of them. Execution trace and sw version are included in zip. (no .nextflow.log for this one, sorry)

Command used and terminal output

No response

Relevant files

pipeline_info.zip

System information

No response

Daniel-VM commented 1 month ago

Hi @SchwarzMarek ,

I have ran -r dev and no issues... Can you try to reproduce this bug?

nextflow run main.nf -profile test,docker --annotation_tool bakta --baktadb_download true --outdir results

Image

SchwarzMarek commented 1 month ago

Hi, still no luck...

.nextflow.log

Image

Daniel-VM commented 1 month ago

It seems something went wrong with the assembly step in sample ERR044595. Was the FASTA file generated correctly? There is no value under the # contig column for this sample.

SchwarzMarek commented 1 month ago

I can't see anything wrong with the assembly step. I noticed this issue when I wanted more precise annotation than those provided by prokka and did rerun with bakta. With prokka, I had annotations for every sample. One thing to note is that I was using full bakta db then (and also for this test data here).

I'm uploading the full multiqc report. multiqc.zip

Best Marek

Daniel-VM commented 1 month ago

Got it! Thanks for testing it out. If possible, please review it here: https://github.com/nf-core/bacass/pull/178