convert_matrix_from_mtx_to_loom:102 - ValueError: Length mismatch: Expected axis has 3 elements, new values have 2 elements

[smoe]

Hello,
I run into this error while running through your build tests of what is tagged as version 1.1.6.

$ cat /home/moeller/git/med-team/pigx/pigx-scrnaseq/tests/out/Log/WT_HEK_4h_br1.hg19.convert_matrix_from_mtx_to_loom.log
beignet-opencl-icd: no supported GPU found, this is probably the wrong opencl-icd package for this hardware
(If you have multiple ICDs installed and OpenCL works, you can ignore this message)
Parsing gene ids from gtf file /home/moeller/git/med-team/pigx/pigx-scrnaseq/tests/out/Annotation/hg19/hg19.gtf
Reading input files ...
Counts
Features ...
Traceback (most recent call last):
  File "/home/moeller/git/med-team/pigx/pigx-scrnaseq/scripts/convert_matrix_from_mtx_to_loom.py", line 102, in <module>
    genes.columns = ['gene_id','gene_id2']
  File "/usr/lib/python3/dist-packages/pandas/core/generic.py", line 5287, in __setattr__
    return object.__setattr__(self, name, value)
  File "pandas/_libs/properties.pyx", line 67, in pandas._libs.properties.AxisProperty.__set__
  File "/usr/lib/python3/dist-packages/pandas/core/generic.py", line 661, in _set_axis
    self._data.set_axis(axis, labels)
  File "/usr/lib/python3/dist-packages/pandas/core/internals/managers.py", line 177, in set_axis
    raise ValueError(
ValueError: Length mismatch: Expected axis has 3 elements, new values have 2 elements

which was invoked in this context:

Error in rule convert_matrix_from_mtx_to_loom:
    jobid: 0
    output: /home/moeller/git/med-team/pigx/pigx-scrnaseq/tests/out/Mapped/WT_HEK_4h_br1/hg19/WT_HEK_4h_br1_hg19_UMI.matrix.loom
    log: /home/moeller/git/med-team/pigx/pigx-scrnaseq/tests/out/Log/WT_HEK_4h_br1.hg19.convert_matrix_from_mtx_to_loom.log (check log file(s) for error message)

RuleException:
CalledProcessError in line 37 of /home/moeller/git/med-team/pigx/pigx-scrnaseq/scripts/Accessory_Functions.py:                                                                                                                                                                                                                 
Command 'set -euo pipefail;  /usr/bin/python3 /home/moeller/git/med-team/pigx/pigx-scrnaseq/scripts/convert_matrix_from_mtx_to_loom.py --sample_id WT_HEK_4h_br1 --input_dir /home/moeller/git/med-team/pigx/pigx-scrnaseq/tests/out/Mapped/WT_HEK_4h_br1/hg19/WT_HEK_4h_br1_Solo.out --gtf_file /home/moeller/git/med-team/pigx/pigx-scrnaseq/tests/out/Annotation/hg19/hg19.gtf --star_output_types_keys Gene GeneFull Velocyto Velocyto --star_output_types_vals Counts GeneFull Spliced Unspliced --output_file /home/moeller/git/med-team/pigx/pigx-scrnaseq/tests/out/Mapped/WT_HEK_4h_br1/hg19/WT_HEK_4h_br1_hg19_UMI.matrix.loom --sample_sheet_file /home/moeller/git/med-team/pigx/pigx-scrnaseq/tests/sample_sheet.csv --path_script /home/moeller/git/med-team/pigx/pigx-scrnaseq/scripts &> /home/moeller/git/med-team/pigx/pigx-scrnaseq/tests/out/Log/WT_HEK_4h_br1.hg19.convert_matrix_from_mtx_to_loom.log' returned non-zero exit status 1.                                
  File "/usr/lib/python3/dist-packages/snakemake/executors/__init__.py", line 2168, in run_wrapper                                                                                                                                                                                                                             
  File "/home/moeller/git/med-team/pigx/pigx-scrnaseq/Snake_Dropseq.py", line 769, in __rule_convert_matrix_from_mtx_to_loom                                                                                                                                                                                                   
  File "/home/moeller/git/med-team/pigx/pigx-scrnaseq/scripts/Accessory_Functions.py", line 37, in print_shell                                                                                                                                                                                                                 
  File "/usr/lib/python3/dist-packages/snakemake/executors/__init__.py", line 529, in _callback                                                                                                                                                                                                                                
  File "/usr/lib/python3.8/concurrent/futures/thread.py", line 57, in run                                                                                                                                                                                                                                                      
  File "/usr/lib/python3/dist-packages/snakemake/executors/__init__.py", line 515, in cached_or_run                                                                                                                                                                                                                            
  File "/usr/lib/python3/dist-packages/snakemake/executors/__init__.py", line 2199, in run_wrapper                                                                                                                                                                                                                             
Exiting because a job execution failed. Look above for error message

Would you have any immediate idea for me on what to check/change? As a disclaimer, I am running this with Debian packages, not with guix. But all dependencies should be very recent and build-tested themselves.

Many thanks and regards
Steffen