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metaQuantome: Expand (Taxonomy Analysis Mode) [GalaxyP] #47

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alialhaid opened this issue Feb 23, 2023 · 0 comments
Open

metaQuantome: Expand (Taxonomy Analysis Mode) [GalaxyP] #47

alialhaid opened this issue Feb 23, 2023 · 0 comments

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@alialhaid
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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).

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