Hello,
I am trying to run this command but am getting an error that my metadata.tsv file is not a file.
Here is what I ran:
qiime feature-table summarize
–i-table home/gtbui/Documents/EXP30/qiime2-analysis/dada2_trim_33_280/table.qza
–o-visualization home/gtbui/Documents/EXP30/qiime2-analysis/dada2_trim_33_280/table.qzv
–m-sample-metadata-file home/gtbui/Documents/EXP30/metadata.tsv
–verbose
This is the error
Traceback (most recent call last):
File “/opt/anaconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/click/type.py”, line 163, in _convert_metadata
artifact = qiime2.Artifact.load(fp)
File “/opt/anaconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/result.py”, line 66, in load
archiver = archive.Archiver.load(filepath)
File “/opt/anaconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/core/archive/archiver.py”, line 299, in load
archive = cls.get_archive(filepath)
File “/opt/anaconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/core/archive/archiver.py”, line 259, in get_archive
raise ValueError("%s does not exist." % filepath)
ValueError: home/gtbui/Documents/EXP30/metadata.tsv does not exist.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/opt/anaconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/click/type.py”, line 166, in _convert_metadata
metadata = qiime2.Metadata.load(fp)
File “/opt/anaconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/metadata/metadata.py”, line 309, in load
return MetadataReader(filepath).read(into=cls,
File “/opt/anaconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/metadata/io.py”, line 47, in init
“(not a directory): %s” % filepath)
qiime2.metadata.io.MetadataFileError: 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): home/gtbui/Documents/EXP30/metadata.tsv
There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org
Find details on QIIME 2 metadata requirements here: Metadata in QIIME 2 — QIIME 2 2019.10.0 documentation
**I have triple-checked my file’s path and that is not the issue here. There might be something wrong with my metadata.tsv file itself? I have used this file with cutadapt for the following code with no issues: **
qiime cutadapt demux-single
–i-seqs /home/gtbui/Documents/EXP30/qiime2-analysis/multiplexed_seqs.qza
–m-barcodes-file /home/gtbui/Documents/EXP30/metadata.tsv
–m-barcodes-column BarcodeSequence
–p-error-rate 0
–o-per-sample-sequences /home/gtbui/Documents/EXP30/qiime2-analysis/demultiplexed_seqs.qza
–o-untrimmed-sequences /home/gtbui/Documents/EXP30/qiime2-analysis/untrimmed_seqs.qza
–verbose
I am new to 16S analysis so am very appreciative of any type of help. Thank you!