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geronimp / enrichM

Toolbox for comparative genomics of MAGs
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ERROR while classifying using custom module #116

Closed ShailNair closed 3 years ago

ShailNair commented 3 years ago

Hi, I created a tsv file with nitrogen fixation KO's, when I run the classify command I get the following error-

/home/mcs/miniconda3/envs/enrichm-0.5.0/bin/enrichm classify --output /home/mcs/gene/shail/metagenomics/CLEANED_FILES/sunbeam_decontaminated/leptolyngbya_cleaned/sunbeam_output/qc/decontam/binning_all_togather/binning/metwrap_mod/enrichM/classify_n2fix --genome_and_annotation_matrix /home/mcs/gene/shail/metagenomics/CLEANED_FILES/sunbeam_decontaminated/leptolyngbya_cleaned/sunbeam_output/qc/decontam/binning_all_togather/binning/metwrap_mod/enrichM/annotate/ko_frequency_table.tsv --custom_modules /home/mcs/gene/shail/metagenomics/CLEANED_FILES/sunbeam_decontaminated/leptolyngbya_cleaned/sunbeam_output/qc/decontam/binning_all_togather/binning/metwrap_mod/enrichM/N2.tsv [2020-12-17 09:39:36 AM] INFO: Running the classify pipeline [2020-12-17 09:39:36 AM] INFO: Reading in custom modules: /home/mcs/gene/shail/metagenomics/CLEANED_FILES/sunbeam_decontaminated/leptolyngbya_cleaned/sunbeam_output/qc/decontam/binning_all_togather/binning/metwrap_mod/enrichM/N2.tsv [2020-12-17 09:39:36 AM] INFO: Read in annotations for 125 genomes Traceback (most recent call last): File "/home/mcs/miniconda3/envs/enrichm-0.5.0/bin/enrichm", line 342, in run.run_enrichm(args, sys.argv) File "/home/mcs/miniconda3/envs/enrichm-0.5.0/lib/python3.6/site-packages/enrichm/run.py", line 317, in run_enrichm args.genome_and_annotation_matrix, args.output) File "/home/mcs/miniconda3/envs/enrichm-0.5.0/lib/python3.6/site-packages/enrichm/classifier.py", line 109, in classify_pipeline path = ModuleDescription(pathway_string) File "/home/mcs/miniconda3/envs/enrichm-0.5.0/lib/python3.6/site-packages/enrichm/module_description_parser.py", line 37, in init = ModuleDescriptionParser().parse_module_string(module_description_string) File "/home/mcs/miniconda3/envs/enrichm-0.5.0/lib/python3.6/site-packages/enrichm/module_description_parser.py", line 263, in parse_module_string "Parse exception on %s" % string) Exception: Parse exception on "(K02586,K02588,K02591)"

Attached are the ko_frequency.tsv and custom module file files.zip

geronimp commented 3 years ago

Hi,

Thank you for your interest in enrichM, sorry for the late reply. The custom module file is mis-formatted. The quotation marks are not necessary, so if you remove them it should run fine.

Thanks,

Joel

ShailNair commented 3 years ago

Thanks. somehow creating the custom module in ms excel included these quotation marks.