Hey!
I recently switched from a mac to pc and now i am trying to run qiime2 in wsl ubuntu.
I have major problems with creating the manifest file... seems like it might be the wrong format or something. I tried saving it as a tab deliminated .txt file.
Here is my code
qiime tools import --type SampleData[PairedEndSequencesWithQuality] --input-path manifest10.txt --output-path demux.qza --input-format PairedEndFastqManifestPhred33
This is the error i keep getting;
There was a problem importing manifest10.txt:
manifest10.txt is not a(n) PairedEndFastqManifestPhred33 file:
Found header on line 1 with the following labels: ['sample-id\tabsolute-filepath\tdirection'], expected: ['sample-id', 'absolute-filepath', 'direction']
this is an example file path in my manifest:
/home/justyna/qiime2/Sophie/1_raw_data/B1_1_R1.fastq
Hi @justh and @crusher083,
I don't agree that this post constitutes a code of conduct violation. I apologize if this created any confusion. @cherman2 is sitting next to me and mentioned that she'll be happy to help with this @justh, so she will follow up with you here.
Thank you! When i transfer the raw reads to my old mac, create a manifest file there, and import data as demux.qza it works no problem. But when i do the same on PC then i have some weird formatting issue with my manifest file
Hi @justh!
Welcome to the forum!
It looks like your issue is here:
It is expecting a comma separated file and it looks like yours is tab separated. If you changed the tabs to comma's this should work.
Also, This is the original version of a manifest file but this v1 manifest was a bit more error prone so we now have switched to a v2 manifest. Here is our tutorial about how to make that v2 manifest. Importing data — QIIME 2 2023.2.0 documentation
I hope that helps! Let me know if you run into any errors while importing! Importing your data into is always the hardest part!
!