search

ncbi / sra-tools

SRA Tools
Other
1.07k stars 243 forks source link

`--fasta-unsorted` causes fasterq-dump to quit with error code 3 #935

Closed linsalrob closed 2 days ago

linsalrob commented 1 month ago

Trying to download some SRA data, if I use

$ fasterq-dump  SRR25692597

the download succeeds:

spots read      : 134,337
reads read      : 268,674
reads written   : 268,674

However, if I just download the fasta-unsorted data, I get an error:

$ fasterq-dump  --fasta-unsorted SRR25692597
2024-05-08T03:27:49 fasterq-dump.3.1.0 err: data unexpected while reading file within network system module - Cannot KStblHttpFileTimedReadChunked
2024-05-08T03:36:17 fasterq-dump.3.1.0 err: the input data is missing the READ-column
fasterq-dump quit with error code 3

I confirmed that report cloud instance identity is unchecked (for both AWS and GCP) in vdb-config -i as reported in issue #588 and that there is sufficient disk space (because exporting fastq files worked).

klymenko commented 1 month ago

run prefetch SRR25692597 first.