Error during smk-pipeline: "fibertools: error: unrecognized arguments: --nuc-size-cutoff 85"

[NurislamSheih]

Hi @mrvollger,

I've faced with a problem during running-smk the pipeline:

Error in rule nucleosome:
    jobid: 257
    input: temp/m64323e_220412_060446_resdir/ft.43-of-80.bam, temp/m64323e_220412_060446_resdir/hmm_model.json
    output: temp/m64323e_220412_060446_resdir/nuc.43-of-80.bam
    log: logs/m64323e_220412_060446_resdir/nucleosome/43-of-80.log (check log file(s) for error details)
    conda-env: fiberseq-smk
    shell:

        fibertools -t 4 add-nucleosomes                 -m temp/m64323e_220412_060446_resdir/hmm_model.json --nuc-size-cutoff 85                 -i temp/m64323e_220412_060446_resdir/ft.43-of-80.bam -o temp/m64323e_220412_060446_resdir/nuc.43-of-80.bam                 2> logs/m64323e_220412_060446_resdir/nucleosome/43-of-80.log

        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: 63493901
Logfile logs/m64323e_220412_060446_resdir/nucleosome/43-of-80.log:
=============================================================================================================================================================================================================================================================
/home/nshaikhutdinov/miniconda3/envs/fiberseq-smk/lib/python3.10/site-packages/xgboost/compat.py:36: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead.
  from pandas import MultiIndex, Int64Index
usage: fibertools [-h] [-t THREADS] [-v] [-V]
                  {bam2bed,add-m6a,add-nucleosomes,model,split,trackhub,bed2d4}
                  ...
fibertools: error: unrecognized arguments: --nuc-size-cutoff 85
=============================================================================================================================================================================================================================================================

Error executing rule nucleosome on cluster (jobid: 257, external: 63493901, jobscript: /net/seq/pacbio/test_tmp/fiberseq/more27_bam_files/.snakemake/tmp.7bkajxy6/snakejob.nucleosome.257.sh). For error details see the cluster log and the log files of the involved rule(s).

I am still trying to figure out what happened; smk pipeline worked without errors during the last few days. Could it be some version discrepancy between xgboost and pandas?

[mrvollger]

Hi @NurislamSheih ,

Looks like your fibertools version got out of date with the fiberseq-smk pipeline (I recently added that new paramater). When you are in the conda env you can update with:

yes | pip uninstall fibertools && pip install git+https://github.com/fiberseq/fibertools; fibertools -h 

This will soon be versioned so thing like this don't happen but for now I recommend this.

keep me in the loop about how this goes.

[NurislamSheih]

Oh, thank you a lot, Mitchell! Sure!