Francesca Bernini
03/19/2024, 12:51 PMERROR ~ 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...pontus
03/19/2024, 2:42 PM