Phred33 import problem ' "forward-absolute-filepath" could not be found '

[LotteG (Lotte)]

Hi everyone!

I want to import files with the manifest format, but even after checking with the forum on the problem I don't seem to get any further. I'm using the root of the absolute path to show where my file 33 manifest file is located, but I keep running into this problem:

Filepath on line 1 and column "forward-absolute-filepath" could not be found ($mnt/c/Users/Lotte/PycharmProjects/envsetup/Data_group_A/RawAS
/A.S.M9.raw_1.fq) for sample "A.S.M9".

I checked the manifest file in google spreadsheet with Keemei and it said that it was fine... Here is my code:

qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path /mnt/c/Users/Lotte/PycharmProjects/envsetup/Data_group_A/RawAS/se-33-manifest.tsv
--output-path paired-end-demux.qza
--input-format PairedEndFastqManifestPhred33V2

And I'll add a picture of my manifest file as well:

If someone could help me out, it would be much appreciated!

Kind regards,
Lotte

[thermokarst]

Hi @LotteG!

@LotteG

I’m using the root of the absolute path to show where my file 33 manifest file is located, but I keep running into this problem

If that is the case, then there appears to be a small typo in your manifest file. You have $mnt/c/Users..... at the start of each filepath, but it looks like you should replace the $ with a /: /mnt/c/Users......

Give that a shot and let us know how it goes!

[LotteG (Lotte)]

Hi Matthew,

It was indeed the manifest file, thanks so much!

Kind regards,
Lotte