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`--eliminate-quals` issue in `prefetch` #883

Closed padix-key closed 1 month ago

padix-key commented 7 months ago

When I run prefetch -O . --eliminate-quals ERR11344941, I get

2023-11-26T14:24:52 prefetch.3.0.6: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2023-11-26T14:24:53 prefetch.3.0.6: 1) Downloading 'ERR11344941'...
2023-11-26T14:24:53 prefetch.3.0.6: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2023-11-26T14:24:53 prefetch.3.0.6:  Downloading via HTTPS...
2023-11-26T14:24:57 prefetch.3.0.6:  HTTPS download succeed
2023-11-26T14:24:57 prefetch.3.0.6 int: path not found while renaming directory within file system module - cannot rename /path/to/ERR11344941/ERR11344941.sra.tmp to /path/to/ERR11344941/ERR11344941.sra
2023-11-26T14:24:57 prefetch.3.0.6: 1) failed to download 'ERR11344941': RC(rcFS,rcDirectory,rcRenaming,rcPath,rcNotFound)

The SRA file is not created.

This issue does not appear when I omit --eliminate-quals.

klymenko commented 7 months ago

@padix-key, why do you use --eliminate-quals?

padix-key commented 5 months ago

Hi, sorry for the late response. Downstream I use fasterqdump, but I would like to extract only the sequences as FASTA. Hence, I do not need to download the quality scores in prefetch.

klymenko commented 4 months ago

@padix-key, that you for your report.

We are going to change behavior of prefetch when --eliminate-quals is specified. It will enforce download of SRA Lite files, or fail if not available. If SRA Lite files is not available you will have to use full quality run.

klymenko commented 4 months ago

New toolkit with change of prefetch with --eliminate-quals was released.