FastQ file import taking a very long time


I am trying to import my FASTQ files for analysis but the command has been running for nearly 48hrs now! I'm currently using QIIME2 (2021.8) via Virtual Box I do have a lot of reads within the files (I'm not sure if that slows down the import process) but only 102 files in total. I haven't received an error message but I am concerned as from what I've read on other forums this is a very long time for this command to run!

The command running is:

qiime tools import
--type ‘SampleData[PairedEndSequencesWithQuality]’
--input-path 'home/qiime2/Documents/FASTQ_ALL'
--input-format CasavaOneEightSingleLanePerSampleDirFmt
--output-path demux-paired-end.qza

Thank you for any advice!!

Hi @Laura1,

Welcome to the :qiime2: forum!

This command can take some time (depending on the size of your files) - but 48 hours does seem a bit long. Since posting this, how long did the process take to completion (if you didn't stop the command from running)? A good investigative test would be to re-run this command with maybe 3 or 4 files and see how long it takes to run those - this could give us a better idea of where the delay is coming from (if it's not purely related to the file size/number of files).

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