Faster way to create Manifest File using VME with Linux operating system? (New to Qiime2)

[cgregg1227 (Collin Gregg)]

I’m currently creating a manifest file to input approximately 400 16S samples into Qiime2. So far I’ve had to manually create a file pathway for each samples forward and reverse read. Is there a faster way to do this?

Thanks,
Collin

[jwdebelius (Justine Debelius)]

Hi @cgregg1227,

Two options:

1. The manifest generator
2. If you have a sequence mapping that isn’t easily pulled from the filename, you could write some python or R code to name the files. (This, of course, depends on you already having a mapping between the ID you want to use at the end and something about the file name.)

Best,
Justine

[cgregg1227 (Collin Gregg)]

Thank you for the quick response! I tried option one, but I continue to get this error "found unrecognized ID column name" when inputting the manifest file created from the manifest generator. Do you have any suggestions for how to fix this?

Thank you,

Collin

[cgregg1227 (Collin Gregg)]

This was the command I put in as well:

qiime tools import
–type 'SampleData{PairedEndSequenceWithQualtiy] ’
–input-path /path/to/file
–output-path paired-end-demux.qza
–input-format PairedEndFastqManifestPhred33V2

[jwdebelius (Justine Debelius)]

Hi @cgregg1227,

I haven’t used the manifest generator, but it looks like you need to add the header row. I can never remember the exact spelling off the top of my head, but check out the manifest documentation. You might also want to open an issue in community plugin support to contact the developer about a potential bug.

Best,
Justine

[cgregg1227 (Collin Gregg)]

I had tried to put a header row in, but that led to another error that my file was not in UTF-8 format. I’ll go ahead and post in the community plugin support as well. Thank you for all the help and suggestons!

Best,
Collin