Error importing Ion Torrent SingleEndFastqPhred33V2 Data

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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.

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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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