DRAM-v distill Error

[YiFANzZhou]

Hi,

after running a DRAM-v annotate job, I tried to use the DRAM-v "distill" module to summarize the annotation results, and it returns an error:

$ DRAM-v.py distill -i /yifan/DRAM/results/annotations.tsv -o /DRAM/dram_v_distill
0:00:00.088643: Retrieved database locations and descriptions
Traceback (most recent call last):
File "/homes/yizhou/miniconda3/envs/DRAM/lib/python3.10/site-packages/pandas/core/indexes/base.py", line 3621, in get_loc
return self._engine.get_loc(casted_key)
File "pandas/_libs/index.pyx", line 136, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/index.pyx", line 163, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 5198, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 5206, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'auxiliary_score'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/homes/yizhou/miniconda3/envs/DRAM/bin/DRAM-v.py", line 153, in
args.func(**args_dict)
File "/homes/yizhou/miniconda3/envs/DRAM/lib/python3.10/site-packages/mag_annotator/summarize_vgfs.py", line 235, in summarize_vgfs
potential_amgs = filter_to_amgs(annotations, max_aux=max_auxiliary_score,
File "/homes/yizhou/miniconda3/envs/DRAM/lib/python3.10/site-packages/mag_annotator/summarize_vgfs.py", line 49, in filter_to_amgs
vmap_aux_check = ('V' not in amg_flags) and ('M' in amg_flags) and (row['auxiliary_score'] <= max_aux) and
File "/homes/yizhou/miniconda3/envs/DRAM/lib/python3.10/site-packages/pandas/core/series.py", line 958, in getitem
return self._get_value(key)
File "/homes/yizhou/miniconda3/envs/DRAM/lib/python3.10/site-packages/pandas/core/series.py", line 1069, in _get_value
loc = self.index.get_loc(label)
File "/homes/yizhou/miniconda3/envs/DRAM/lib/python3.10/site-packages/pandas/core/indexes/base.py", line 3623, in get_loc
raise KeyError(key) from err
KeyError: 'auxiliary_score'

Could you help me solve this?

THANK YOU

Yifan

[rmFlynn]

What was your DRAM-v annotate command? It looks like you may not have used the -v argument and thus did not add in Virsorter data necessary to make the auxiliary_score field.

[YiFANzZhou]

hi, yes, i have not used the -v option.

i use virsorter2 to identify the virus sequences. it seems that the result files do not contain a VIRSorter_affi-contigs.tab output file.

only these three: final-viral-boundary.tsv final-viral-combined.fa final-viral-score.tsv

what information does the VIRSorter_affi-contigs.tab contain? can I use one of the above three to replace it?

thank you!!

[rmFlynn]

You need to run Virsorter2 with the --prep-for-dramv option. Here is a protocol that should be mostly up-to-date.

[YiFANzZhou]

thank you!!!