MOB-recon v3.1.7 fails at the biomarker stage.

[ejurga]

MOB-recon v3.1.7 fails when running create_biomarker_dataframe. Previous versions (tested on v3.1.4) are working on the same set of contigs.

Full stack trace:

Traceback (most recent call last):
  File "/home/emil/Projects/mobsuite-rgi/work/conda/mob_suite_3.1.7/bin/mob_recon", line 10, in <module>
    sys.exit(main())
  File "/home/emil/Projects/mobsuite-rgi/work/conda/mob_suite_3.1.7/lib/python3.8/site-packages/mob_suite/mob_recon.py", line 1472, in main
    biomarker_df = create_biomarker_dataframe(biomarker_params,id_mapping,logging)
  File "/home/emil/Projects/mobsuite-rgi/work/conda/mob_suite_3.1.7/lib/python3.8/site-packages/mob_suite/utils.py", line 1397, in create_biomarker_dataframe
    return pd.concat(data_frames)
  File "/home/emil/Projects/mobsuite-rgi/work/conda/mob_suite_3.1.7/lib/python3.8/site-packages/pandas/core/reshape/concat.py", line 271, in concat
    op = _Concatenator(
  File "/home/emil/Projects/mobsuite-rgi/work/conda/mob_suite_3.1.7/lib/python3.8/site-packages/pandas/core/reshape/concat.py", line 329, in __init__
    raise ValueError("No objects to concatenate")
ValueError: No objects to concatenate

This is using mamba to create an environment.

Command run:

DB=/path/to/mob/database/directory
mob_recon \
	--infile contigs.fasta \
	--outdir mobSuite \
	--num_threads 1 \
	--database_directory $DB \
	--force 

I have attached the contigs I used.
contigs.fasta.zip

[kbessonov1984]

Hi,
I will need to look at this issue and it has to do with empty list of dataframes that need to be concatenated to generate a master table of plasmid features with respective coordinates. Effectively you are getting pandas error similar to pd.concat([]). This means that your sample has most likely no detected plasmid features or plasmids at all (had no time to test your inputs yet). This biomarker_dataframe was a new feature introduced only in version 3.1.7. Will address this edge case in the next release and push a patch meanwhile that would be available via source code installation. Since you already have all dependencies installed, then install from source code will be very painless.

[ejurga]

Sounds good! I'll use the earlier versions in the meantime.

I'll leave the issue open for now in case others run into the same problem.

[kbessonov1984]

fixed in v3.1.8 release