q2 manifest file error

Technical Support
1

Hello qiime2 users ,

im trying to use qiime 2 and it refuses to run with the manifest file i'v made ; i uploaded it
[V1V2_platax_manifest.

txt|attachment](upload://5iGny3cRe2Zkoh1iYwPFQVu1649.txt) (4.0 KB)

here 's the error :

ERROR: /home1/datawork/alambard/platax_data/MI_M03992_0637_001_FLD0361_J0-31_Pas_A_12_V1V2_R1.fastq.gz from q2_manifest not exit. Wrong path?

the path is correct and the file exists , checked it by running ls command . i changed the file names and recreated an new folder .
i have no idea what's wrong about this q2_manifest error

i would happreciate any help , tank you .

2

I wonder if this could be a formatting error that's confusing Qiime2.

Would you be willing to post your manifest file so we can take a look?

3

i corrected this error by changing the folder path and created a new one to store the data

but i still got one :

ERROR: q2_manifest and q2_metadata did not have the same number of lines

i crated the files using open office calc on ubuntu
a formattting issue could be the problem indeed but i dont see how exactlty

here are the 2 files : qiime_input - Google Drive

4

OK great!

Oh no!

I took a look at the files and I'm not sure what's going on.

  • They have the same number of lines
  • All sample IDs are the same
    (I tested this with sort <file> | cut -f1 | shasum)

I'm stumped here. My only idea is that qiime is still looking at the wrong files, but you just checked that...

EDIT: Can you post the full command and your version of Qiime2 you ran so we can take a look?

6

Hi @scipio04,

I'm curious what your actual command was, along with the machine you're using and your version of QIIME 2. I haven't come across this error message before, but I think those details above will give us a clue as to where things are going sideways. Thanks! :lizard:

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7

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