Comments (5)
This is because of a problem with the Singularity container. A certain generation of containers was built with a Busybox that had a broken /etc/resolv.conf
. I have reported this to the Galaxy folks who build the Singularity containers and will follow up once that is fixed.
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Could be intermittent network or server issues. ENA/SRA do see a lot of traffic.
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I'm experiencing the same issue with wget using the dev branch, were you able to get this to work?
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I think the problem is the container.
$ module load singularity-ce/4.1.0
$ singularity shell depot.galaxyproject.org-singularity-wget-1.20.1.img
WARNING: Skipping mount /var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
Singularity> wget -t 5 -nv -c -T 60 -O ERX2235404_ERR2179103_2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/ERR217/003/ERR2179103/ERR2179103_2.fastq.gz
wget: unable to resolve host address 'ftp.sra.ebi.ac.uk'
However, if I try the latest version of the container (check https://depot.galaxyproject.org/singularity/):
$ singularity pull https://depot.galaxyproject.org/singularity/wget:1.21.4
$ singularity shell wget\:1.21.4
Singularity> wget -t 5 -nv -c -T 60 -O ERX2235404_ERR2179103_2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/ERR217/003/ERR2179103/ERR2179103_2.fastq.gz
Singularity> ls ERX2235404_ERR2179103_2.fastq.gz
ERX2235404_ERR2179103_2.fastq.gz
So, I guess the solution is to instruct Nextflow to fetch the latest image in modules/local/sra_fastq_ftp/main.nf
:
conda "conda-forge::wget=1.20.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/wget:1.20.1' :
'biocontainers/wget:1.20.1' }"
change to (conda also for consistency but I haven't test):
conda "conda-forge::wget=1.21.4"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/wget:1.21.4' :
'biocontainers/wget:1.21.4' }"
from fetchngs.
sorry, just realized that the suggested change already made it to the dev branch :p
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Related Issues (20)
- TypeError: unsupported operand type(s) for |: 'dict' and 'dict' HOT 1
- error executing process HOT 3
- Add compatibility with sarek samplesheet
- SRAtools download seems to insert paired-end suffix into workdir path HOT 6
- Support .ngc file for dbgap downloads HOT 2
- FEAT: Pass scientific name as input to download the data
- Pipeline fails for large studies HOT 1
- Pipeline crashes if some samples are not available HOT 3
- Use nf-test for input validation
- check out extensions for input files HOT 1
- Add ability to download more than 2 FastQ files via FTP and Aspera HOT 3
- Merge technical replicates (SRR1 + SRR2 -> SRX)
- nf-validation-1.1.3: Operation not supported HOT 20
- `vdb-validate` does not detect file corruption HOT 5
- URGENT: pin nf-validation version HOT 1
- aspera `CONDA_PREFIX` error HOT 1
- Automatic retrieval of input id.csv from test-datasets for test profile HOT 5
- SRA file links deprecated HOT 3
- Support for GSA accessions
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