Error importing manifest file; paired end, demultiplexed data

[tannerbahm]

Hi! I'm trying to import demultiplexed, paired end sequences via a manifest file.

This is the code I have been running:
qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path /Users/tannerbahm/Desktop/sequence_manifest.csv --output-path /Users/tannerbahm/Desktop/paired-end-demux.qza --input-format PairedEndFastqManifestPhred33V2

This is the error code I receive:
There was a problem importing /Users/tannerbahm/Desktop/sequence_manifest.csv:

/Users/tannerbahm/Desktop/sequence_manifest.csv is not a(n) PairedEndFastqManifestPhred33V2 file:

Found unrecognized ID column name 'sample-id,absolute-filepath,direction' 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'

NOTE: Metadata files must contain tab-separated values.

I'm using qiime2 version 2024.5 on my Mac terminal. If someone could help out I would appreciate it!

[Oddant1 (Anthony Simard)]

Hello @tannerbahm, it looks like you used a comma separated values or .csv file. Your metadata file must be a tab separated values or .tsv file. The formatting is the same as .csv but with tabs separating the columns where you have commas.

[tannerbahm]

I am trying to import a manifest file instead of a metadata file, are those supposed to be tab separated?

[colinbrislawn (Colin J Brislawn)]

Yeah, both are supposed to use tabs.

It's a Tab Separated Value file after all!

There are many ways to do this:

Converting CSV to TSV