Hi, I am trying to download data using fetching fr...
# fetchngs
v
Hi, I am trying to download data using fetching from nf-core and I ran into the following error, could some help me with this please. ERROR ~ Error executing process > 'NFCORE_FETCHNGSSRASRA_FASTQ_FTP (SRX4672080_SRR7820913)' Caused by: Process
NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX4672080_SRR7820913)
terminated with an error exit status (4) Command executed: wget \ -t 5 -nv -c -T 60 \ -O SRX4672080_SRR7820913_1.fastq.gz \ ftp.sra.ebi.ac.uk/vol1/fastq/SRR782/003/SRR7820913/SRR7820913_1.fastq.gz echo "39b1b9d6e6024c6197bce0f588a62562 SRX4672080_SRR7820913_1.fastq.gz" > SRX4672080_SRR7820913_1.fastq.gz.md5 md5sum -c SRX4672080_SRR7820913_1.fastq.gz.md5 wget \ -t 5 -nv -c -T 60 \ -O SRX4672080_SRR7820913_2.fastq.gz \ ftp.sra.ebi.ac.uk/vol1/fastq/SRR782/003/SRR7820913/SRR7820913_2.fastq.gz echo "2aab9c790e848cea43bd5cf777b82cf7 SRX4672080_SRR7820913_2.fastq.gz" > SRX4672080_SRR7820913_2.fastq.gz.md5 md5sum -c SRX4672080_SRR7820913_2.fastq.gz.md5 cat <<-END_VERSIONS > versions.yml "NFCORE_FETCHNGSSRASRA_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: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred INFO: Environment variable SINGULARITYENV_SNIC_TMP is set, but APPTAINERENV_SNIC_TMP is preferred WARNING: Skipping mount /var/lib/apptainer/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container wget: unable to resolve host address 'ftp.sra.ebi.ac.uk' Work dir: /crex/proj/naiss2024-23-81/private/vathsa/gbm/work/32/bae37b1c3fbc077ab0c10578b503ea Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named
.command.sh
-- Check '.nextflow.log' file for details
m
Did you try using another `download_method`: https://nfco.re/fetchngs/1.12.0/parameters#download_method ?
v
Hi Maxime, I cant access the site
👀 2
m
m
I was sure I did a copy paste
🙂 1
v
Thanks I will try it