validateFQ

[hanrong498]

Hi there!

Thanks again for the active development.

I have a problem with the validateFQ in the version 3.0.0. I have the error:

Error in rule validateFQ:
jobid: 26
input: /scratch/hhu/aztekin/AVT0115/allfastqc/15102024_KH_M-96-well_H3K9me3_S17_R1_001.fastq.gz, /scratch/hhu/aztekin/AVT0115/allfastqc/15102024_KH_M-96-well_H3K9me3_S17_R2_001.fastq.gz
output: originalFASTQ/15102024_KH_M-96-well_H3K9me3_S17.valid
conda-env: /tmp/b37fb85caffc0a43a642143270acfbca_
shell:

fq lint /scratch/hhu/aztekin/AVT0115/allfastqc/15102024_KH_M-96-well_H3K9me3_S17_R1_001.fastq.gz /scratch/hhu/aztekin/AVT0115/allfastqc/15102024_KH_M-96-well_H3K9me3_S17_R2_001.fastq.gz
touch originalFASTQ/15102024_KH_M-96-well_H3K9me3_S17.valid

(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
error: arg: function not defined: lint/0

However, this job is okay in version 2.8.0 (it can proceed just fine). Is there any difference in the fq version 0.10.0 (for snakePipes v2.8.0) and 0.11.0 (for v3.0.0)?

Thanks again!

Hanrong

[WardDeb]

Hi,

Thanks for the report. This is due to the 'fq' package in conda-forge being different software then in bioconda..
The latest master branch (tag 3.1.0) has this fixed, full release will still follow !
In the meantime you could either roll back to an earlier installation (though note that a fresh env install will display the same problem), or install the latest version via cloning the repo and using pip to install the latest version.

Hope this helps !