Hello, I'm new to nextflow and I'm trying to run f...
# fetchngs
f
Hello, I'm new to nextflow and I'm trying to run fetchngs with the test profile on the cluster but, I always get the following error
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ERROR ~ Error executing process > 'NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9626017_SRR13191702)'                                                                                                                                                                                                                                                          Caused by:                                                                                                                                                                    Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9626017_SRR13191702)` terminated with an error exit status (4)                                                                                                                                                                                                                                         Command executed:                                                                                                                                                                                                                                                                                                                                         wget \                                                                                                                                                                          -t 5 -nv -c -T 60 \                                                                                                                                                         -O SRX9626017_SRR13191702_1.fastq.gz \                                                                                                                                      <http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz|ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz>                                                                                                                                                                                                                                                                          echo "89c5be920021a035084d8aeb74f32df7  SRX9626017_SRR13191702_1.fastq.gz" > SRX9626017_SRR13191702_1.fastq.gz.md5                                                          md5sum -c SRX9626017_SRR13191702_1.fastq.gz.md5                                                                                                                                                                                                                                                                                                         wget \                                                                                                                                                                          -t 5 -nv -c -T 60 \                                                                                                                                                         -O SRX9626017_SRR13191702_2.fastq.gz \                                                                                                                                      <http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz|ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz>                                                                                                                                                                                                                                                                          echo "56271be38a80db78ef3bdfc5d9909b98  SRX9626017_SRR13191702_2.fastq.gz" > SRX9626017_SRR13191702_2.fastq.gz.md5                                                          md5sum -c SRX9626017_SRR13191702_2.fastq.gz.md5                                                                                                                                                                                                                                                                                                         cat <<-END_VERSIONS > versions.yml                                                                                                                                          "NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP":                                                                                                                                            wget: $(echo $(wget --version | head -n 1 | sed 's/^GNU Wget //; s/ .*$//'))                                                                                            END_VERSIONS                                                                                                                                                                                                                                                                                                                                          Command exit status:                                                                                                                                                          4                                                                                                                                                                                                                                                                                                                                                     Command output:                                                                                                                                                               (empty)                                                                                                                                                                                                                                                                                                                                               Command error:                                                                                                                                                                WARNING: Skipping mount /nfs/software/as/el7.2/EasyBuild/CRG/software/Singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container                                                                                                                                                                wget: unable to resolve host address '<http://ftp.sra.ebi.ac.uk|ftp.sra.ebi.ac.uk>'
I've tried to use both
--download-method
available without success... can someone help me? The command line I use is
nextflow run nf-core/fetchngs -r 1.12.0 -profile test,singularity --download-method aspera -bg --outdir test_test >test.log
The problem is that when I execute the
wget
command in the interactive terminal everything works correctly...