Error importing Ion Torrent SingleEndFastqPhred33V2 Data

Hi there! I am getting the following error when trying to import my Ion Torrent samples into QIIME2. Note they have been subjected to ITSxperss.

When I run qiime tools import --input-path /isilon/cfia-ottawa-fallowfield/users/girouxeml/gladishd/pirl_working/OW_S5-0143-161/qiime2_import_manifest.tsv --output-path /isilon/cfia-ottawa-fallowfield/users/girouxeml/gladishd/pirl_working/OW_S5-0143-161/qiime2/demix-single-end.qza --input-format SingleEndFastqManifestPhred33V2

I get error output: "There was a problem importing /isilon/cfia-ottawa-fallowfield/users/girouxeml/gladishd/pirl_working/OW_S5-0143-161/qiime2_import_manifest.tsv:

/scratch/q2-SingleLanePerSampleSingleEndFastqDirFmt-qo9hb3zd/OW-ITSF-2020-161-Plate114-208-B73_72_L001_R1_001.fastq.gz is not a(n) FastqGzFormat file:

Missing sequence for record beginning on line 9"

Please note that I am running qiime2-2021.2 in a conda environment.

I am not sure where to go. I have done many analyses like this before using similarly formatted manifest files but now it is not working for some reason. I will appreciate any help.

Thank you in advance for your time.

Hello Dan,

Strange! Would you be willing to post the first 20 lines of that file so we could take a look and see what’s wrong?

You could use a command like this:

gzip -dc /path/to/file/OW-ITSF-2020-161-Plate114-208-B73_72_L001_R1_001.fastq.gz | head -n 20

I’m wondering if the files got messed up during download, and this will let us check!

Colin

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