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fasterq-dump error #909

Closed linsson closed 3 months ago

linsson commented 4 months ago

Hi. I'm having problems recovering fastq files from 11 accessions:

SRR8640104 SRR8640113 SRR8640126 SRR8640135 SRR8640138 SRR8640142 SRR8640152 SRR8640160 SRR8640164 SRR8640166 SRR8640178

Apparently the error occurs after prefetch-ing when I try to use fastq-dump to recover fastq files.

$ vdb-validate SRR8640178 2024-02-19T08:25:59 vdb-validate.3.0.10 info: Database 'SRR8640178.sra' metadata: md5 ok 2024-02-19T08:25:59 vdb-validate.3.0.10 info: Table 'SEQUENCE' metadata: md5 ok 2024-02-19T08:26:00 vdb-validate.3.0.10 info: Column 'ALTREAD': checksums ok 2024-02-19T08:26:00 vdb-validate.3.0.10 info: Column 'QUALITY': checksums ok 2024-02-19T08:26:01 vdb-validate.3.0.10 info: Column 'READ': checksums ok 2024-02-19T08:26:33 vdb-validate.3.0.10 info: Database 'SRR8640178.sra' is consistent

$ fasterq-dump SRR8640178 2024-02-19T08:26:57 fasterq-dump.3.0.10 err: insp_read_len().VCursorCellDataDirect( NAME ) -> RC(rcSRA,rcColumn,rcReading,rcRow,rcNull)

An error occurred during processing. A report was generated into the file '/home/aprea/ncbi_error_report.txt'. If the problem persists, you may consider sending the file to 'sra-tools@ncbi.nlm.nih.gov' for assistance.

fasterq-dump quit with error code 3

ncbi_error_report.txt

Am I missing something?

Thank you.

durbrow commented 4 months ago

There seems to be a problem with the data file for SRR8640104. We are investigating.

durbrow commented 3 months ago

There are problems with the data. We have requested that they get reloaded. You can email sra@ncbi.nlm.nih.gov with this issue. They may be able to keep you up-to-date on the reload process.