qiime tools import: manifest not parsing as tsv

[nick-youngblut]

I'm using q2cli version 2021.4.0 installed via conda, but getting the following error:

  Found header on line 1 with the following labels: ['sample-id\tforward-absolute-filepath\treverse-absolute-filepath'], expected: ['sample-id', 'absolute-filepath', 'direction']

...when I run:

qiime tools import \
  --type 'SampleData[PairedEndSequencesWithQuality]' \
  --input-format PairedEndFastqManifestPhred33 \
  --input-path manifest.tsv \
  --output-path output.qza

According to the docs, the manifest should be tab-delimited, correct?

Also, when I use a comma-delim manifest, the manifest seems to be parsed correctly, but then I get:

expected: ['sample-id', 'absolute-filepath', 'direction']

...while the docs show that ['sample-id', 'forward-absolute-filepath', 'reverse-absolute-filepath'] should work.

If I use:

sample-id,absolute-filepath,direction
SRS1247010,/scratch/SRR3099496/R1.fq,forward
SRS1247010,/scratch/SRR3099496/R2.fq,reverse

...the import job completes successfully.

I believe that I'm using the newest version of qiime2, so I'm a bit puzzled about the apparent mismatch between the docs and the actual usage.

[jwdebelius (Justine Debelius)]

Hi @nick-youngblut,

Try the PairedEndFastqManifestPhred33V2 format instead. That's the TSV version.

Best,
Justine

[nick-youngblut]

Thanks @jwdebelius! I was missing the V2