Automatically re-annotate PFAM domains if they are incompatible

[susheelbhanu]

Hi,

I'm running version 0.1.26 and I'm getting the same error as #47

part of error message is below:

ERROR   06/07 22:04:58   pfam_id
Traceback (most recent call last):
  File "/mnt/data/sbusi/antismash/.snakemake/conda/bf12a359/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 2656, in get_loc
    return self._engine.getloc(key)
  File "pandas/_libs/index.pyx", line 108, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/index.pyx", line 132, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/hashtable_class_helper.pxi", line 1601, in pandas._libs.hashtable.PyObjectHashTable.get_item
  File "pandas/_libs/hashtable_class_helper.pxi", line 1608, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'pfam_id'

Thank you for your help!

[prihoda]

Hi @susheelbhanu, are you able to share the input file and the input command you are using?

[susheelbhanu]

Hi,

Sure, here's the command below and two of the files having the same issue are attached.
GL_R1_GL5_UP_1_C1.3.1_sub.merged.gbk.txt
GL_R80_GL56_UP_1_maxbin_res.049.fasta_sub.merged.gbk.txt

I added the .txt extension to get past the upload file type limitations.

(date && deepbgc pipeline /mnt/data/sbusi/antismash/results/gbk/GL_R80_GL56_UP_1_maxbin_res.049.fasta_sub/GL_R80_GL56_UP_1_maxbin_res.049.fasta_sub.merged.gbk -o $(dirname /mnt/data/sbusi/antismash/results/merged_deepbgc/GL_R80_GL56_UP_1_maxbin_res.049.fasta_sub/GL_R80_GL56_UP_1_maxbin_res.049.fasta_sub.bgc.tsv) && date)

Thank you!

[prihoda]

Ok, this seems to be caused by incompatible PFAM_domain annotations in the GenBank file. Can you turn this into a nucleotide FASTA and run deepbgc pipeline on that? This will re-annotate the Pfam domains using DeepBGC which should fix the issue.

I will rename this ticket, hopefully we can fix this issue later, in the meantime please try the FASTA input.