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#This is the metaQuantome: Expand command line for Taxonomic analysis>>>
tar -xf '/data/dnb07/galaxy_db/files/e/1/3/dataset_e13df1a4-cd88-4fb9-a696-b0224d9bb5d1.dat' && metaquantome expand --data_dir ./data --samps '/data/dnb07/galaxy_db/files/5/c/2/dataset_5c222ea9-1a86-41fb-948a-9378137356d3.dat' --mode 't' --int_file='/data/dnb07/galaxy_db/files/4/9/4/dataset_4942f842-38fe-4d9e-a666-3af0ddb752a3.dat' --pep_colname_int='peptide' --tax_file='/data/dnb07/galaxy_db/files/4/a/8/dataset_4a857575-d203-4036-af4d-181693d0edf1.dat' --pep_colname_tax='peptide' --tax_colname='taxon_id' --outfile='/data/jwd02f/main/056/568/56568584/outputs/galaxy_dataset_aae7ac64-3010-488f-a1e6-3548d810ec9f.dat'
#This is the error output>>>
Traceback (most recent call last):
File "/usr/local/tools/_conda/envs/[email protected]/bin/metaquantome", line 33, in
sys.exit(load_entry_point('metaquantome==2.0.2', 'console_scripts', 'metaquantome')())
File "/usr/local/tools/_conda/envs/[email protected]/lib/python3.6/site-packages/metaquantome/cli.py", line 33, in cli
nopep_file=args.nopep_file, ft_tar_rank=args.ft_tar_rank)
File "/usr/local/tools/_conda/envs/[email protected]/lib/python3.6/site-packages/metaquantome/modules/expand.py", line 55, in expand
results = taxonomy_analysis(df=df, samp_grps=samp_grps, data_dir=data_dir, tax_colname=tax_colname)
File "/usr/local/tools/_conda/envs/[email protected]/lib/python3.6/site-packages/metaquantome/modules/taxonomy_analysis.py", line 31, in taxonomy_analysis
results = metaquantome.modules.expand.common_hierarchical_analysis(ncbi, df_clean, tax_colname, samp_grps)
File "/usr/local/tools/_conda/envs/[email protected]/lib/python3.6/site-packages/metaquantome/modules/expand.py", line 86, in common_hierarchical_analysis
samp_annot.add_samples_from_df(df, annot_colname, samp_grps)
File "/usr/local/tools/_conda/envs/[email protected]/lib/python3.6/site-packages/metaquantome/classes/SampleAnnotations.py", line 38, in add_samples_from_df
hier.add_nodes_from_df(filt, annot_colname, samp)
File "/usr/local/tools/_conda/envs/[email protected]/lib/python3.6/site-packages/metaquantome/classes/AnnotationHierarchy.py", line 43, in add_nodes_from_df
self._add_node_with_ancestors(term, intensity)
File "/usr/local/tools/_conda/envs/[email protected]/lib/python3.6/site-packages/metaquantome/classes/AnnotationHierarchy.py", line 61, in _add_node_with_ancestors
ancestors = self.db.get_ancestors(term)
File "/usr/local/tools/_conda/envs/[email protected]/lib/python3.6/site-packages/metaquantome/databases/NCBITaxonomyDb.py", line 257, in get_ancestors
num_query_rank = NUMERIC_RANK[rank_of_query]
KeyError: 'strain'
Can someone please explain what is the error means? Expand tool worked fine for Functional Analysis, and Input column formats are all the same (i.e peptide).
The text was updated successfully, but these errors were encountered:
#This is the metaQuantome: Expand command line for Taxonomic analysis>>>
tar -xf '/data/dnb07/galaxy_db/files/e/1/3/dataset_e13df1a4-cd88-4fb9-a696-b0224d9bb5d1.dat' && metaquantome expand --data_dir ./data --samps '/data/dnb07/galaxy_db/files/5/c/2/dataset_5c222ea9-1a86-41fb-948a-9378137356d3.dat' --mode 't' --int_file='/data/dnb07/galaxy_db/files/4/9/4/dataset_4942f842-38fe-4d9e-a666-3af0ddb752a3.dat' --pep_colname_int='peptide' --tax_file='/data/dnb07/galaxy_db/files/4/a/8/dataset_4a857575-d203-4036-af4d-181693d0edf1.dat' --pep_colname_tax='peptide' --tax_colname='taxon_id' --outfile='/data/jwd02f/main/056/568/56568584/outputs/galaxy_dataset_aae7ac64-3010-488f-a1e6-3548d810ec9f.dat'
#This is the error output>>>
Traceback (most recent call last):
File "/usr/local/tools/_conda/envs/[email protected]/bin/metaquantome", line 33, in
sys.exit(load_entry_point('metaquantome==2.0.2', 'console_scripts', 'metaquantome')())
File "/usr/local/tools/_conda/envs/[email protected]/lib/python3.6/site-packages/metaquantome/cli.py", line 33, in cli
nopep_file=args.nopep_file, ft_tar_rank=args.ft_tar_rank)
File "/usr/local/tools/_conda/envs/[email protected]/lib/python3.6/site-packages/metaquantome/modules/expand.py", line 55, in expand
results = taxonomy_analysis(df=df, samp_grps=samp_grps, data_dir=data_dir, tax_colname=tax_colname)
File "/usr/local/tools/_conda/envs/[email protected]/lib/python3.6/site-packages/metaquantome/modules/taxonomy_analysis.py", line 31, in taxonomy_analysis
results = metaquantome.modules.expand.common_hierarchical_analysis(ncbi, df_clean, tax_colname, samp_grps)
File "/usr/local/tools/_conda/envs/[email protected]/lib/python3.6/site-packages/metaquantome/modules/expand.py", line 86, in common_hierarchical_analysis
samp_annot.add_samples_from_df(df, annot_colname, samp_grps)
File "/usr/local/tools/_conda/envs/[email protected]/lib/python3.6/site-packages/metaquantome/classes/SampleAnnotations.py", line 38, in add_samples_from_df
hier.add_nodes_from_df(filt, annot_colname, samp)
File "/usr/local/tools/_conda/envs/[email protected]/lib/python3.6/site-packages/metaquantome/classes/AnnotationHierarchy.py", line 43, in add_nodes_from_df
self._add_node_with_ancestors(term, intensity)
File "/usr/local/tools/_conda/envs/[email protected]/lib/python3.6/site-packages/metaquantome/classes/AnnotationHierarchy.py", line 61, in _add_node_with_ancestors
ancestors = self.db.get_ancestors(term)
File "/usr/local/tools/_conda/envs/[email protected]/lib/python3.6/site-packages/metaquantome/databases/NCBITaxonomyDb.py", line 257, in get_ancestors
num_query_rank = NUMERIC_RANK[rank_of_query]
KeyError: 'strain'
Can someone please explain what is the error means? Expand tool worked fine for Functional Analysis, and Input column formats are all the same (i.e peptide).
The text was updated successfully, but these errors were encountered: