Error when using kneaddata from anaconda

Infrastructure and utilities KneadData
1

kneaddata v0.12.0

When installing kneaddata from anaconda there are two errors that occur when using it:

  • trimmomatic in anaconda is a python wrapper script, so it gives the next error: Error: Invalid or corrupt jarfile /A2/danielpalma/mambaforge/envs/kneaddata/bin/trimmomatic
  • It doesn’t remove adapters, since the default parameters for trimmomatic when using kneaddata --help are [ DEFAULT : MINLEN:60 ILLUMINACLIP:/-SE.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:50 ] I think that it is not recognizing correctly the adapters folder
2

Did you solved this problem, I have the same problem as your first question

3

Not exactly, I just used --bypass-trim and run the trimming by itself. I had multiple errors when running kneaddata (v0.12 from bioconda) so here are some considerations:

  • if you use --bypass-trim then --run-trim-repetitive is also skipped.
  • if the FASTQs have a description in addition to the id it will throw an error
  • I had to change the names of the paired files to the next format NAME.1.fastq.gz and NAME.2.fastq.gz or it will throw an error