Dear Friends,
when trying to generate qzv file:
qiime diversity alpha-group-significance --i-alpha-diversity core-metrics-results/shannon_vector.qza --m-metadata-file cDNA_1to11_metadat.tsv --o-visualization core-metrics-results/shannon_vector.qzv
Plugin error from diversity:
All numbers are identical in kruskal
Debug info has been saved to /tmp/qiime2-q2cli-err-0_qhw_zp.log
The temp file shows this error:
Traceback (most recent call last):
File "/root/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/commands.py", line 274, in call
results = action(**arguments)
File "</root/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/decorator.py:decorator-gen-389>", line 2, in alpha_group_significance
File "/root/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/root/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 427, in callable_executor
ret_val = self._callable(output_dir=temp_dir, **view_args)
File "/root/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_diversity/_alpha/_visualizer.py", line 92, in alpha_group_significance
kw_H_all, kw_p_all = scipy.stats.mstats.kruskalwallis(*groups)
File "/root/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/scipy/stats/mstats_basic.py", line 1237, in kruskal
raise ValueError('All numbers are identical in kruskal')
ValueError: All numbers are identical in kruskal
Metadata file is:
#SampleID BarcodeSequence LinkerPrimerSequence BodySite Year Month Day Subject ReportedAntibioticUsage DaysSinceExperimentStart Description
#q2:types categorical categorical categorical numeric numeric numeric categorical categorical numeric categorical
ww_1_cDNA Barcode1 GGACTACNVGGGTWTCTAAT_GTGYCAGCMGCCGCGGTAA metadata 2018 10 28 subject-001 Yes 0 subject-1.gut.2018-10-28
ww_2_cDNA Barcode2 GGACTACNVGGGTWTCTAAT_GTGYCAGCMGCCGCGGTAA metadata 2018 10 28 subject-002 Yes 0 subject-1.gut.2018-10-28
ww_3_cDNA Barcode3 GGACTACNVGGGTWTCTAAT_GTGYCAGCMGCCGCGGTAA metadata 2018 1 20 subject-003 No 2 subject-2.gut.2018-1-20
ww_4_cDNA Barcode4 GGACTACNVGGGTWTCTAAT_GTGYCAGCMGCCGCGGTAA metadata 2018 2 28 subject-004 Yes 0 subject-1.gut.2018-10-28
ww_6_cDNA Barcode5 GGACTACNVGGGTWTCTAAT_GTGYCAGCMGCCGCGGTAA metadata 2018 3 20 subject-006 No 0 subject-2.gut.2018-1-20
ww_7_cDNA Barcode6 GGACTACNVGGGTWTCTAAT_GTGYCAGCMGCCGCGGTAA metadata 2018 4 28 subject-007 Yes 0 subject-1.gut.2018-10-28
ww_8_cDNA Barcode7 GGACTACNVGGGTWTCTAAT_GTGYCAGCMGCCGCGGTAA metadata 2018 5 20 subject-008 No 4 subject-2.gut.2018-1-20
ww_9_cDNA Barcode8 GGACTACNVGGGTWTCTAAT_GTGYCAGCMGCCGCGGTAA metadata 2018 6 28 subject-009 Yes 0 subject-1.gut.2018-10-28
ww_10_cDNA Barcode9 GGACTACNVGGGTWTCTAAT_GTGYCAGCMGCCGCGGTAA metadata 2018 7 20 subject-0010 No 5 subject-2.gut.2018-1-20
ww_11_cDNA Barcode10 GGACTACNVGGGTWTCTAAT_GTGYCAGCMGCCGCGGTAA metadata 2018 8 28 subject-0011 Yes 0 subject-1.gut.2018-10-28
I would really appreciate your comments on solving this issue? thanks!