Class attribute error during multi-sample run

[Krannich479]

Hi, I am getting the following error when I try to run Pamir:

Creating a new project folder... OK
Checking binary pre-requisites...  ... OK
Sorting bam file... SKIPPING
Extracting FASTQ from Alignment file... SKIPPING
Masking Reference Genome... OK
Traceback (most recent call last):
  File "/path/to/pamir/pamir.py", line 1448, in <module>
    sys.exit(main())
  File "/path/to/pamir/pamir.py", line 1438, in main
    run_command(config)
  File "/path/to/pamir/pamir.py", line 1005, in run_command
    index(config)
  File "/path/to/pamir/pamir.py", line 327, in index
    cmd           = pipeline.mrsfast + ' --index  {0} --ws {1}'.format(input_file, config.get("mrsfast","window_size") )
AttributeError: class pipeline has no attribute 'mrsfast'

and indeed class pipeline has no such attribute.

My call was:

/path/to/pamir/pamir.py
    -p /path/to/workdir/results
    -r /path/to/genome_ins.fa
    --files mrsfast-best-search=/path/to/workdir/sorted_bams/

Can you tell what's going on here? Is the call valid? Input bams are name-sorted.

(Mabye important) Sidenote: The folder /path/to/workdir/sorted_bams/ does not really contain mappings from mrsFast but BWA. I was told ages ago that --files mrsfast-best-search can also handle BWA bam files, please correct me if I am wrong here.

I also tried a run with --files alignment=\<aln1>.bwa,\<aln2>.bwa,...,\<alnN>.bwa but that one never started. I am trying to call something like your README's example (2) or (3).

Thanks!

[Krannich479]

I think I can close this anyway since the CLI got a general makeover.