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"fasterq-dump.3.0.7 err: the input data is missing the QUALITY-column" BUT sra QUALITY column is present. #851
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GabeAl
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fasterq-dump.3.0.7 err: the input data is missing the QUALITY-column
"fasterq-dump.3.0.7 err: the input data is missing the QUALITY-column" BUT quality column is present
Sep 12, 2023
GabeAl
changed the title
"fasterq-dump.3.0.7 err: the input data is missing the QUALITY-column" BUT quality column is present
"fasterq-dump.3.0.7 err: the input data is missing the QUALITY-column" BUT sra QUALITY column is present.
Sep 12, 2023
I am having the same problem. I am running fasterq-dump in a snakemake workflow. Weirdly. when i run without specifying a temp directory (which uses default) OR when I direct my home (~/temp-fasterq-dump). I get no errors. I am thinking it might be a permssion or directory lock problem maybe? Important notes
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This misbehavior happens with fasterq-dump 3.0.7 on the following accession and a few others, at a rate of about 7% of biosample-based accessions. SAMN08049698 and some other biosample-based accessions fail, but most work fine including within the same project. Interestingly, the underlying run in this case (SRR6468610) still works fine.
Why this is a bug:
A workaround could be manually using entrez direct or something to translate into Run IDs, dumping the Run IDs, renaming (or concatenating) to biosample IDs again. But that's quite the workaround for the couple of files this fails on, so I thought I'd report it here.
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