I'm trying to run nfcore/fetchngs https://nf-co.re/fetchngs/1.11.0 (singularity+slurm ) with an input only containing SRX10474968 and with --force_sratools_download
all my processes FASTERQDUMP fail:
8 a0/971d51 3250085 NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX10474968_SRR14103032) FAILED 3 2024-01-24 22:05:49.415 29.9s 25s - - - --
9 20/a9ce28 3250087 NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX10474968_SRR14103035) FAILED 3 2024-01-24 22:05:54.398 1m 20s 50s - - - --
10 67/4c125b 3250089 NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX10474968_SRR14103033) FAILED 3 2024-01-24 22:05:54.507 1m 20s 50s - - - --
11 2e/785287 3250091 NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX10474968_SRR14103034) FAILED 3 2024-01-24 22:05:59.398 1m 15s 50s - - - --
with a .command.err starts with:
Error: fasterq-dump cannot create this file: '(...)/2e/785287648c6a7c99e4acada7006045/SRX10474968_SRR14103034'
Error: fasterq-dump cannot create this file: '(...)/2e/785287648c6a7c99e4acada7006045/SRX10474968_SRR14103034'
spots read : 46,524,055
reads read : 93,048,110
the command in .command.sh is:
export NCBI_SETTINGS="$PWD/user-settings.mkfg"
fasterq-dump \
--split-files --include-technical \
--threads 6 \
--outfile SRX10474968_SRR14103033 \
\
SRR14103033
(...)
how can I fix this please ?
cross-posted: https://nfcore.slack.com/archives/C024915L4KB/p1706130702887529
•
written
by
Pierre Lindenbaum
2 answers
looks like a bug in SRA: https://github.com/ncbi/sra-tools/issues/865
I am currently trying to download a couple of raw sequencing data files using sra-tools prefetch and fasterq-dump. Prefetch works fine but I get a weird error when trying to convert the generated *.sra file to fastq with fasterq-dump. The data is paired-end and the actual path should be /scratch/daniel.malzl/work/aa/7ab6e5d29db7a0352a1f1cd4af2af3/SRX10737613_SRR14385311 but judging by the error message there seems to be some bug in the renaming code because it says the following:
yes, the scratch partition where I can work is my email.... :-P
/scratch/nautilus/users/mynamep@univ-nantes.fr/work/....
On our cluster, you need to use cache = 'lenient' in the nextflow config to get around timing problems with the shared network storage which lead to similar errors.
Alternatively, do you have file number limits on your working directory?
sorry that didn't work.
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Not helping, but why all the overhead with such a pipeline when you can enter the accession at sra-explorer.info and get a wget link? It could not be any easier!
ATpoint yes, but in real life I've got ~200 accessions numbers :-P . Furthermore, If I can setup such 'simple' pipeline on our new cluster, then I can run more complicated workflows like SAREK... :-)