Vathsa
04/12/2024, 9:38 AMNFCORE_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 detailsMaxime Garcia
04/12/2024, 4:12 PMVathsa
04/15/2024, 7:15 AMmashehu
04/15/2024, 7:22 AMMaxime Garcia
04/15/2024, 7:23 AMVathsa
04/15/2024, 7:25 AM