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fasterq-dump: cannot create this file, full path is changed with `_1` and `_2` #899

Open lindenb opened 5 months ago

lindenb commented 5 months ago

Hi all,

I'm trying to run fasterq-dump 3.0.8 via the nfcore/fetchngs workflow. Whenever I try to run fasterq-dump the workflow raises an error with the following message:

Command error:                                                                                                                                 

        Error: fasterq-dump cannot create this file: '/scratch/nautilus/users/me@univ-nantes.fr/work/NEXTFLOW/2024/202310123.xxxx_2.GRCh38/work/
STEP1/SRA/71/fd281d46f664e7c9a993412a7a9086/SRX10474968_SRR14103035'

        Error: fasterq-dump cannot create this file: '/scratch/nautilus/users/me@univ-nantes.fr/work/NEXTFLOW/2024/202310123.xxxx_1.GRCh38/work/
STEP1/SRA/71/fd281d46f664e7c9a993412a7a9086/SRX10474968_SRR14103035'
  spots read      : 46,172,755                    
  reads read      : 92,345,510

the script below is launched in /scratch/nautilus/users/me@univ-nantes.fr/work/NEXTFLOW/2024/202310123.xxxx.GRCh38/work/STEP1/SRA/71/fd281d46f664e7c9a993412a7a9086/.command.sh:

export NCBI_SETTINGS="$PWD/user-settings.mkfg"

fasterq-dump \
    --split-files --include-technical \
    --threads 6 \
    --outfile SRX10474968_SRR14103035 \
     \
    SRR14103035

I'm also suprised about the path the tool is trying to create: why are _1 and _2 are added in the middle of the path ?

(...) /202310123.xxxx_1.GRCh38/work/STEP1/SRA/71/fd281d46f664e7c
                      ^
                      |
lindenb commented 5 months ago

looks like a duplicate of: https://github.com/ncbi/sra-tools/issues/865