Basic fasterq-dump command is failing from `SIGNAL

Basic fasterq-dump command is failing from `SIGNAL - Segmentation fault`

Does anyone know how to get around this error?

Here's my versions:

(base) -bash-4.1$ fasterq-dump -h | tail -n 2
/usr/local/devel/ANNOTATION/jespinoz/anaconda3/bin/fasterq-dump : 2.10.0

(base) -bash-4.1$ fastq-dump -h | tail -n 2
/usr/local/devel/ANNOTATION/jespinoz/anaconda3/bin/fastq-dump : 2.10.0

Here's my command:

(base) -bash-4.1$ fasterq-dump -t 4 ERR599092

Here's my error:

2020-01-17T22:52:55 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_uint8_array( #166936577 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2020-01-17T22:52:55 fasterq-dump.2.10.0 err: row #166936577 : READ.len(202) != QUALITY.len(0) (F)
2020-01-17T22:52:55 fasterq-dump.2.10.0 fatal: SIGNAL - Segmentation fault

sequencing

• 3,171 views • link

updated 6.6 years ago by ATpoint

• written 6.6 years ago by O.rka

1 answer

This can be anything. It indicates a difference in read length and quality length but if this is an error from the tool or at NCBI is hard to say. fastq-dump (or its follow-up versions) were never stable enough for downloading. Therefore one typically uses prefetch first to download the sra file and then converts to fastq with fastq-dump. Still, it can be way faster to download directly as fastq as described in:

Fast download of FASTQ files from the European Nucleotide Archive (ENA)

Alternatively, for a single file you can simply enter it in sra-explorer and get the download link for direct fastq download from there. The links the tool provides are based on the above tutorial. For the fast download via Aspera check the tutorial towards how to set it up.

• 0 views • link

written 6.6 years ago by ATpoint