Like that title says I am having trouble following the Atacama soil microbiome tutorial. More specifically I am having trouble with one step that I can’t seem to get past. The command is:
qiime tools export
–input-path demux-subsample.qzv
–output-path ./demux-subsample/
qiime demux filter-samples
–i-demux demux-subsample.qza
–m-metadata-file ./demux-subsample/per-sample-fastq-counts.tsv
–p-where ‘CAST([forward sequence count] AS INT) > 100’
–o-filtered-demux demux.qza
The first part of the command works fine but the second part throws out this error: "There was an issue with loading the file ./demux-subsample/per-sample-fastq-counts.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): ./demux-subsample/per-sample-fastq-counts.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: https://docs.qiime2.org/2019.10/tutorials/metadata/
"
I looked in the file that the first command created and there is no .tsv file like the error said but there is a .csv file with the same name. So I tried changing the .tsv in the second command to a .csv and I got this error: "There was an issue with loading the file ./demux-subsample/per-sample-fastq-counts.csv as metadata:
Found unrecognized ID column name ‘sample_name,SampleID’ while searching for header. The first column name in the header defines the ID column, and must be one of these values:
Case-insensitive: ‘feature id’, ‘feature-id’, ‘featureid’, ‘id’, ‘sample id’, ‘sample-id’, ‘sampleid’
Case-sensitive: ‘#OTU ID’, ‘#OTUID’, ‘#Sample ID’, ‘#SampleID’, ‘sample_name’
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: https://docs.qiime2.org/2019.10/tutorials/metadata/"
So what can I do to make this command work and move on with the tutorial. Thank you in advance
