When I run the wmgx_wmtx workfllow, tasks related to rna_dna_norm.py fail. I am using the example dataset for wmgx_wmtx provided on the github.
This is the command I am using:
biobakery_workflows wmgx_wmtx --input-metagenome input_wms --input-metatranscriptome input_wts --input-mapping mapping.tsv --output output_wmtx --qc-options “–trimmomatic /home/jxx419/miniconda3/envs/biobakery_workflow_envs/share/trimmomatic/ --bypass-trf” --bypass-strain-profiling
These are the resulting errors for task 64 and 65 respectively:
File “/home/jxx419/miniconda3/envs/biobakery_workflow_envs/bin/rna_dna_norm.py”, li
ne 180, in write_file\n file_handle.write(“\t”.join(column_labels)+“\n”)\nTypeError: a by
tes-like object is required, not 'str'\n’
and
File “/home/jxx419/miniconda3/envs/biobakery_workflow_e
nvs/bin/rna_dna_norm.py”, line 132, in divide_by_sample_total_abundance\n for j in range(le
n(data[0])):\nIndexError: list index out of range\n’
I tried changing this line:
with open(file, “wb”) as file_handle:
to this:
with open(file, “w”) as file_handle:
as recommended in this post: Wmgx_wmtx worfklow rna_dna_norm.py failure + why is metagenome needed in metatranscriptome analysis?
but it did not work. I have no clue as to what the issue could be. Again, I am using the exact data as provided in the examples folder in github. Any help would be greatly appreciated, thank you!