Error when importing via manifest file

Hello, I’m trying to import my sequences by this command:
qiime tools import --type ‘sampleData[PairedEndSequencesWithQuality]’
–input-path se-33-manifest1
–output-path demux.qza
–input-format PairedEndFastqManifestPhred33
Then I get this error:
(1/1) Invalid value for “–input-path”: Path “se-33-manifest1” is not
even when using the file downloaded from the qiime tutorial the same erro occurs.

Can some one help me please?

Hi @Fabio_Leal_Viana_Bon,

Welcome to the :qiime2: forum!

Could you please try the command pwd and the ls. You should see se-33-manifest1 in the result of ls. If not, try moving the file to your current directory or moving to the directory with the file in it.

If it is there, can you run head se-33-manifest1?


Hi, the file is already on the directory, So I execute:
head se-33-manifest1

and It returns:
“permission denied”

So I did:
sudo head se-33-manifest1
and it opened the file:
# single-end PHRED 33 fastq manifest file for forward reads

tryng to import again, but the same erro occurs :confused:

Hi @Fabio_Leal_Viana_Bon,

The permissions issue is a new one for me. It sounds like you’re possibly on your own computer, but you might be working out of a folder that’s hard to modify. If you’re comfortable with the path, then try

chmod +777 se-33-manifest1

which should change the permissions.


Thank you, it’s solved the problem. Yes I’m using Ubuntu LTS on my computer, this may be an issue?
Now I’m getting this error:
Semantic type sampleData[PairedEndSequencesWithQuality] does not have a compatible directory format.

But a believe it’s a subject for other topic : ), Thanks again.

1 Like

This should be SampleData[PairedEndSequencesWithQuality], but yes, I agree, if you have more issues, please open up a new topic!


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