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fasterq-dump unable to convert sra file to fasta #929

Closed krisma2002 closed 5 months ago

krisma2002 commented 5 months ago

Hi All,

I am trying to use fasterq-dump to extract fasta files for this accession ERR260142, but failed. Whether I re-download the sra file or update the sra-tools version, it doesn't work! The error shows as follows:

2024-04-19T07:52:47 fasterq-dump.3.1.0 err: cmn_iter.c cmn_read_uint8_array( #10452993 ).VCursorCellDataDirect() -> RC(rcXF,rcFunction,rcExecuting,rcBuffer,rcInsufficient) 2024-04-19T07:52:47 fasterq-dump.3.1.0 err: row #10452993 : READ.len(202) != QUALITY.len(0) (F) spots read : 2,022,351 reads read : 4,044,702 reads invalid : 1

An error occurred during processing. A report was generated into the file 'C:\Users\Kris Ma/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

Any advice would be appreciated!

durbrow commented 5 months ago

Try it again.

prefetch ERR260142
fasterq-dump --split-3 ERR260142

Don't remove ERR260142.sra from the ERR260142 directory. Don't use the path to the .sra file. Just prefetch and dump. That is how it is intended to work. Or, because this is a small unaligned accession, you could use fastq-dump --skip-technical with negligible loss of performance:

fastq-dump --skip-technical --split-3 ERR260142

krisma2002 commented 5 months ago

@durbrow Well received. This problem was solved perfectly. Thanks!