Hi team ,
I have this error (qiime2-amplicon-2024.5) qiime composition ancombc \
--i-table /dss/work/suga8254/ampliseq/merged_results/filtered-A_crassa-table_genus.qza
--m-metadata-file /dss/work/suga8254/ampliseq/merged_results/merged_metadata.tsv
--p-formula 'Sample_type + Environment'
--p-reference-levels "Sample_type::Feces Environment::Feces"
--verbose
--o-differentials /dss/work/suga8254/ampliseq/merged_results/ancombc-Sample_type_Environment_Feces_A_crassa-genus.qza
filtered-A_crassa-table_genus.qza (229.2 KB)
merged_metadata.tsv (6.5 KB)
Traceback (most recent call last):
File "/user/suga8254/.conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 520, in __call__
results = self._execute_action(
File "/user/suga8254/.conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 581, in _execute_action
results = action(**arguments)
File "<decorator-gen-31>", line 2, in ancombc
File "/user/suga8254/.conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self._callable_executor_(
File "/user/suga8254/.conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 576, in _callable_executor_
output_views = self._callable(**view_args)
File "/user/suga8254/.conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_composition/_ancombc.py", line 41, in ancombc
return _ancombc(
File "/user/suga8254/.conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_composition/_ancombc.py", line 195, in _ancombc
raise ValueError(message)
ValueError: Value provided in `reference_levels` parameter not found in the associated column within the metadata. Please make sure each column::value pair is present within the metadata file.
column::value pair with a value that was not found: "Sample_type::Feces Environment::Feces"
NOTE: Your level value appears to contain a `:`, which can be a problem for this action.
Plugin error from composition:
Value provided in `reference_levels` parameter not found in the associated column within the metadata. Please make sure each column::value pair is present within the metadata file.
column::value pair with a value that was not found: "Sample_type::Feces Environment::Feces"
NOTE: Your level value appears to contain a `:`, which can be a problem for this action.
See above for debug info.
I checked metadata file and column and content is there
(qiime2-amplicon-2024.5)
grep "Feces" /dss/work/suga8254/ampliseq/merged_results/merged_metadata.tsv
S63_HA_FE Feces Feces Subject_4 H_atra D atra_S_Feces
S48_HA_FE Feces Feces Subject_4 H_atra D atra_S_Feces
S36_HA_FE Feces Feces Subject_1 H_atra C_D atra_S_Feces
S44_HA_FE Feces Feces Subject_3 H_atra C_D atra_S_Feces
S52_HA_FE Feces Feces Subject_4 H_atra C_D atra_S_Feces
S19_AC_FE Feces Feces Subject_3 A_crassa C_D crassa_S_Feces
S27_AC_FE Feces Feces Subject_4 A_crassa C_D crassa_S_Feces
S15_AC_FE Feces Feces Subject_2 A_crassa C_D crassa_S_Feces
S11_AC_FE Feces Feces Subject_1 A_crassa D crassa_S_Feces
(qiime2-amplicon-2024.5) [suga8254@hpcl002 exported_filtered-A_crassa-table]$ head /dss/work/suga8254/ampliseq/merged_results/merged_metadata.tsv
sampleID Sample_type Environment Subject Species run Group
wA28Mg Midgut Gut Subject_1 H_atra A_B atra_W_Midgut
S33_HA_FG Foregut Gut Subject_1 H_atra D atra_S_Foregut
wC1Fg Foregut Gut Subject_1 A_crassa A_B crassa_W_Foregut
wC16Sg Seagrass Seagrass Seagrass A_crassa B crassa_W_Seagrass
wA34Mg Midgut Gut Subject_3 H_atra B atra_W_Midgut
S63_HA_FE Feces Feces Subject_4 H_atra D atra_S_Feces
wC24SeaW Seawater Seawater Seawater A_crassa B_D crassa_W_Seawater
S43_HA_HG Hingut Gut Subject_3 H_atra D atra_S_Hingut
S28_AC_SE Sediment Sediment Sediment A_crassa C_D crassa_S_Sediment
Could you please help me figure out why the Sample_type::Feces Environment::Feces
is giving me an error ?
Many thanks in advance,
Sabrin