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fasterq-dump.3.1.0 err: the input data is missing the QUALITY-column #924

Closed moldovannorbert closed 3 months ago

moldovannorbert commented 3 months ago

Running v. 3.1.0 on a linux system.

When I run fasterq-dump path/to/dataset/SRX######## I get the error the input data is missing the QUALITY-column.

vdb-validate path/to/file/SRR########.sra -v results in

_2024-03-27T10:01:39 vdb-validate.3.1.0 info: Database 'SRR########.sra' metadata: md5 ok 2024-03-27T10:01:39 vdb-validate.3.1.0 info: Table 'SEQUENCE' metadata: md5 ok 2024-03-27T10:01:39 vdb-validate.3.1.0 info: Column 'ALTREAD': checksums ok 2024-03-27T10:01:39 vdb-validate.3.1.0 info: Column 'QUALITY': checksums ok 2024-03-27T10:01:40 vdb-validate.3.1.0 info: Column 'READ': checksums ok 2024-03-27T10:01:40 vdb-validate.3.1.0 info: Column 'SPOTGROUP': checksums ok 2024-03-27T10:01:40 vdb-validate.3.1.0 info: Database 'path/to/file/SRR########.sra' contains only unaligned reads 2024-03-27T10:01:40 vdb-validate.3.1.0 info: Database 'SRR########.sra' is consistent

Only running fasterq-dump path/to/dataset/path/to/file/SRR########.sra will dump the fastq file.

moldovannorbert commented 3 months ago

Fatal user error... The issue was that I used path/to/dataset/SRX######## not path/to/dataset/SRX########/SRR########.