ANCOM metadata rejection

Hello,
I'm trying to use qiime composition ancom, but when I do, it tells me
"There was an issue with loading the file metadata_LSU_qiime2_2017_bb_only_postme rge.tsv as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): metadata_LSU_qiime2_2017_bb_only_postmerge.tsv

There may be more errors present in the metadata file. To get a full report, s ample/feature metadata files can be validated with Keemei: https://keemei.qiime2 .org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/20 19.7/tutorials/metadata/"

It appears to me that ancom is flat out not recognizing my metadata file. However, I've validated my metadata file with Keemei, and I've used this exact metadata file in other plugins, so I'm not sure why it's not being recognized. In addition, I've verified that this file is located in the directory I'm using. If you'd like to view my metadata, it's here: metadata_LSU_qiime2_2017_bb_only_postmerge.tsv (7.8 KB)

Full command:
qiime composition ancom
--i-table metazoa_grouped_rep_table_comp.qza
--m-metadata-file metadata_LSU_qiime2_2017_bb_only_postmerge.tsv
--m-metadata-column Island
--o-visualization ancom_sheared
--verbose \

Full error output:
Traceback (most recent call last):
File "/opt/anaconda/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q 2cli/click/type.py", line 159, in _convert_metadata
artifact = qiime2.Artifact.load(fp)
File "/opt/anaconda/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q iime2/sdk/result.py", line 66, in load
archiver = archive.Archiver.load(filepath)
File "/opt/anaconda/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q iime2/core/archive/archiver.py", line 299, in load
archive = cls.get_archive(filepath)
File "/opt/anaconda/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q iime2/core/archive/archiver.py", line 259, in get_archive
raise ValueError("%s does not exist." % filepath)
ValueError: metadata_LSU_qiime2_2017_bb_only_postmerge.tsv does not exist.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/opt/anaconda/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q 2cli/click/type.py", line 162, in _convert_metadata
metadata = qiime2.Metadata.load(fp)
File "/opt/anaconda/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q iime2/metadata/metadata.py", line 314, in load
return MetadataReader(filepath).read(into=cls,
File "/opt/anaconda/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q iime2/metadata/io.py", line 47, in init
"(not a directory): %s" % filepath)
qiime2.metadata.io.MetadataFileError: Metadata file path doesn't exist, or the p ath points to something other than a file. Please check that the path exists, ha s read permissions, and points to a regular file (not a directory): metadata_LSU _qiime2_2017_bb_only_postmerge.tsv

There may be more errors present in the metadata file. To get a full report, sam ple/feature metadata files can be validated with Keemei: https://keemei.qiime2.o rg

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2019 .7/tutorials/metadata/

There was an issue with loading the file metadata_LSU_qiime2_2017_bb_only_postme rge.tsv as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): metadata_LSU_qiime2_2017_bb_only_postmerge.tsv

There may be more errors present in the metadata file. To get a full report, s ample/feature metadata files can be validated with Keemei: https://keemei.qiime2 .org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/20 19.7/tutorials/metadata/

See above for debug info."
Thanks.

Whoops! I was working in the wrong directory. My bad. This topic can be taken down if needed.

2 Likes

I was just about to suggest that! I’m glad you figured it out and fixed it.

A post was split to a new topic: Metadata file doesn’t exist