Questions about import formatting and Fastq manifest file

[pzd115]

Hi everyone,

Sorry if this is asked a lot, but I can't seems to figure this out despite looking at many similar forum posts for this....I'm still brand new to this

I was looking to import my fastq files into Qiime2. This is the action I'm putting in the terminal:
qiime tools import \
--type 'SampleData[PairedEndSequencesWithQuality]' \
--input-path stability.files.csv \
--input-format PairedEndFastqManifestPhred33 \
--output-path paired-end-demux.qza

I chose 'SampleData[PairedEndSequencesWithQuality]' since each sample has forward and reverse reads. I put the my csv file as an input. I'm not sure if it is supposed to be PairedEndFastqManifestPhred33 format, since it's giving me this error...

The error I got was:

There was a problem importing stability.files.csv:

stability.files.csv is not a(n) PairedEndFastqManifestPhred33 file

Here's my csv file also: stability.files.csv (1.3 KB)

Any help would be appreciated!

[thermokarst]

Hey there @pzd115 --- you are missing the header for the manifest file, as well, the columns aren't quite right. Check out this section of the docs for guidance:

https://docs.qiime2.org/2018.8/tutorials/importing/#fastq-manifest-formats

Keep us posted!

[pzd115]

I think I fixed some of the formatting, but I'm still getting the same error.

stability.files.csv (2.7 KB)

[thermokarst]

What do you see when you run this command:

ls /Documents

I ask because that is a weird directory location, and I suspect that in fact your files are somewhere like /Users/pzd115/Documents/.

[pzd115]

I'm running it in virtual box, so the path seems different from that.

That is the pwd I'm getting, although I left out the /home/qiime2/ part

[thermokarst]

Yep, exactly — you need to reference the absolute path in your manifest. Just update to match the actual locations on disk and you should be set.

[pzd115]

Still getting the same error message about not being a Phred33 file... Must be some silly mistake I'm doing in the csv file itself?

stability.files.csv (3.1 KB)

[pzd115]

I got it working!! I had the same issue as someone earlier on this forum… I saved mine as CSV UTF-8 (comma delimited) not as a regular CSV (comma separated values)

Thanks again for helping!