problem importing fastq/manifest/manifest.tsv:

Hi,
I am trying to start working with NCBI SRA files for QIIME analysis #version qiime2-2022.2 in conda (Ubuntu 20.04.4 LTS)

while importing data the following error has occurred,

There was a problem importing fastq/manifest/manifest.tsv:

 fastq/manifest/manifest.tsv is not a(n) PairedEndFastqManifestPhred33V2 file:

 There was an issue with loading the metadata file:

..........................................................

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org/

  Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2022.2/tutorials/metadata/

Then, I used kemi for validating the manifest.tsv

After validating again, I try to import the manifest file.
Now I am getting this error message as follow:

There was a problem importing fastq/manifest/manifest.tsv:

  fastq/manifest/manifest.tsv is not a(n) PairedEndFastqManifestPhred33V2 file:

  Filepath on line 12 and column "reverse-absolute-filepath" could not be found ($PWD/fastq/SRR16352452_2.fastq) for sample "SRR16352452".

Can you please help?

Hi @MSrinivasan,

Thanks for reaching out!

Here is where the issue is coming from:

The reverse absolute filepath for sample SRR16352452 could not be found. From the traceback this should be located on line 12 of your manifest file. I'd recommend double checking that this is the correct location for that sample, and that there aren't any typos. If that sample isn't present in your data, you can remove it from your manifest file.

Hope this helps!

Cheers :lizard:

1 Like

@lizgehret Thank you.
Yes. I double-checked that the SRR16352452 reverse file path was not present in the location. Actually, I downloaded an SRA file from the NCBI and split it into fastq files with fastq-dump. I checked the file location and there is no SRR16352452 2. I could not find reverse fastq files for all SRA files.

Hi @MSrinivasan,

Okay, then this is a reasonable explanation for the error message you are seeing! Since that file is missing, you'll need to remove it from the manifest so that it's not looking for a file that doesn't exist. If there are any other missing files that are present in your manifest, you'll need to remove them from the manifest before attempting to re-run your import command. Once that's been cleaned up, you should be all set!

Cheers :lizard:

1 Like

Hi @lizgehret Thank you.

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