Open marcoreverenna opened 7 months ago
Hi Marco,
I think the problem is caused by the space in the reads header: @ERR1713338.1 J00138:63:HCNWCBBXX:1:1101:3772:1103/1
This may cause that the identifiers can not be reformatted correctly. A quick fix is replacing the space by an underscore on the header; e.g sed s/\ /_/g ERR1713338_1.fastq > ERR1713338fixed_1.fastq
Perhaps a long-term solution is creating a module to substitute the space or perhaps substituting Kneaddata by other software where we have more flexibility and can separate the tasks (adapter removal, trimming, host removal, ...). Thinking about ...
The following command line has been used to run the pipeline:
nextflow run main.nf -profile az_test -w az://orange -ansi-log false -resume -with-dag dag.png
This error message occurs after removing the the
path host_genome
in the process QC andindex_ch
in the workflow.This error message occurs after removing the
--reference-db host_genome
inkneaddata
. Seemed the pipeline was running correctly, it did not break since the beginning.