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fetchngs test fails #336

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mjfi2sb3 opened this issue Feb 6, 2025 · 0 comments
Open

fetchngs test fails #336

mjfi2sb3 opened this issue Feb 6, 2025 · 0 comments

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@mjfi2sb3
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mjfi2sb3 commented Feb 6, 2025

I trying the fetchngs pipeline but I can't even get the test to run. Any advice? see log below.

best,
sb

> nextflow run  nf-core/fetchngs -profile test,singularity --outdir test -resume 
Nextflow 24.10.4 is available - Please consider updating your version to it

 N E X T F L O W   ~  version 24.10.2

Launching `https://github.com/nf-core/fetchngs` [nice_jepsen] DSL2 - revision: 8ec2d934f9 [master]

WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`


------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/fetchngs v1.12.0-g8ec2d93
------------------------------------------------------
Core Nextflow options
  revision                  : master
  runName                   : nice_jepsen
  containerEngine           : singularity
  launchDir                 : /cluster/tmp/userx/data
  workDir                   : /cluster/tmp/userx/data/work
  projectDir                : /home/userx/.nextflow/assets/nf-core/fetchngs
  userName                  : userx
  profile                   : test,singularity
  configFiles               : 

Input/output options
  input                     : https://raw.githubusercontent.com/nf-core/test-datasets/2732b911c57e607fa7aea5ba0c3d91b25bafb662/testdata/v1.12.0/sra_ids_test.csv
  outdir                    : test

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function

Max job request options
  max_cpus                  : 2
  max_memory                : 6.GB
  max_time                  : 6.h

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/fetchngs for your analysis please cite:

* The pipeline
  https://doi.org/10.5281/zenodo.5070524

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/fetchngs/blob/master/CITATIONS.md
------------------------------------------------------
executor >  local (33)
[7d/b55df7] process > NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (GSM4907283)                                                            [100%] 10 of 10, cached: 10 ✔
[88/6b13c0] process > NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (6)                                                                     [100%] 10 of 10, cached: 10 ✔
[aa/396e50] process > NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9626017_SRR13191702)                                                     [ 66%] 22 of 33, failed: 22, retries: 22
[7e/0b4955] process > NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:CUSTOM_SRATOOLSNCBISETTINGS (ncbi-settings)   [100%] 1 of 1, cached: 1 ✔
[13/de5c48] process > NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH (SRR14593545)               [100%] 3 of 3, cached: 3 ✔
[c0/7a1127] process > NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX9315476_SRR12848126) [100%] 3 of 3, cached: 3 ✔
[-        ] process > NFCORE_FETCHNGS:SRA:ASPERA_CLI                                                                                 -
[ff/a1cfda] process > NFCORE_FETCHNGS:SRA:SRA_TO_SAMPLESHEET (SRX10940790_SRR14593545)                                               [100%] 3 of 3, cached: 3
[-        ] process > NFCORE_FETCHNGS:SRA:MULTIQC_MAPPINGS_CONFIG                                                                    -
[7c/523396] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)` terminated with an error exit status (4) -- Execution is retried (1)
[fd/42431b] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)` terminated with an error exit status (4) -- Execution is retried (1)
[5b/260cf9] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9504942_SRR13055518)` terminated with an error exit status (4) -- Execution is retried (1)
[79/1e6937] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9504942_SRR13055520)` terminated with an error exit status (4) -- Execution is retried (1)
[ba/64d55e] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9626017_SRR13191702)` terminated with an error exit status (4) -- Execution is retried (1)
[af/c24d1f] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9504942_SRR13055519)` terminated with an error exit status (4) -- Execution is retried (1)
[ce/0091ea] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)` terminated with an error exit status (4) -- Execution is retried (1)
[d5/aa8d48] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (DRX024467_DRR026872)` terminated with an error exit status (4) -- Execution is retried (1)
[37/3c55f5] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9504942_SRR13055517)` terminated with an error exit status (4) -- Execution is retried (1)
[be/3eff92] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX17709227_SRR21711856)` terminated with an error exit status (4) -- Execution is retried (1)
[8f/9abf84] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX17709228_SRR21711855)` terminated with an error exit status (4) -- Execution is retried (1)
[78/a0ac7c] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)` terminated with an error exit status (4) -- Execution is retried (2)
[df/f1c395] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9504942_SRR13055520)` terminated with an error exit status (4) -- Execution is retried (2)
[54/fb07ac] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)` terminated with an error exit status (4) -- Execution is retried (2)
[6e/9d170f] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9504942_SRR13055518)` terminated with an error exit status (4) -- Execution is retried (2)
[cf/8aa6ef] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9504942_SRR13055519)` terminated with an error exit status (4) -- Execution is retried (2)
[40/83ea1d] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9504942_SRR13055517)` terminated with an error exit status (4) -- Execution is retried (2)
[0f/963215] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX17709227_SRR21711856)` terminated with an error exit status (4) -- Execution is retried (2)
[ea/77963a] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)` terminated with an error exit status (4) -- Execution is retried (2)
[a1/405f94] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX17709228_SRR21711855)` terminated with an error exit status (4) -- Execution is retried (2)
[1a/154c02] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (DRX024467_DRR026872)` terminated with an error exit status (4) -- Execution is retried (2)
[d4/58f935] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9626017_SRR13191702)` terminated with an error exit status (4) -- Execution is retried (2)
ERROR ~ Error executing process > 'NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9504942_SRR13055520)'

Caused by:
  Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9504942_SRR13055520)` terminated with an error exit status (4)


Command executed:
executor >  local (33)
[7d/b55df7] process > NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (GSM4907283)                                                            [100%] 10 of 10, cached: 10 ✔
[88/6b13c0] process > NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (6)                                                                     [100%] 10 of 10, cached: 10 ✔
[aa/396e50] process > NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9626017_SRR13191702)                                                     [ 75%] 25 of 33, failed: 25, retries: 22
[7e/0b4955] process > NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:CUSTOM_SRATOOLSNCBISETTINGS (ncbi-settings)   [100%] 1 of 1, cached: 1 ✔
[13/de5c48] process > NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH (SRR14593545)               [100%] 3 of 3, cached: 3 ✔
[c0/7a1127] process > NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX9315476_SRR12848126) [100%] 3 of 3, cached: 3 ✔
[-        ] process > NFCORE_FETCHNGS:SRA:ASPERA_CLI                                                                                 -
[ff/a1cfda] process > NFCORE_FETCHNGS:SRA:SRA_TO_SAMPLESHEET (SRX10940790_SRR14593545)                                               [100%] 3 of 3, cached: 3
[-        ] process > NFCORE_FETCHNGS:SRA:MULTIQC_MAPPINGS_CONFIG                                                                    -
[7c/523396] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)` terminated with an error exit status (4) -- Execution is retried (1)
[fd/42431b] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)` terminated with an error exit status (4) -- Execution is retried (1)
[5b/260cf9] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9504942_SRR13055518)` terminated with an error exit status (4) -- Execution is retried (1)
[79/1e6937] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9504942_SRR13055520)` terminated with an error exit status (4) -- Execution is retried (1)
[ba/64d55e] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9626017_SRR13191702)` terminated with an error exit status (4) -- Execution is retried (1)
[af/c24d1f] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9504942_SRR13055519)` terminated with an error exit status (4) -- Execution is retried (1)
[ce/0091ea] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)` terminated with an error exit status (4) -- Execution is retried (1)
[d5/aa8d48] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (DRX024467_DRR026872)` terminated with an error exit status (4) -- Execution is retried (1)
[37/3c55f5] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9504942_SRR13055517)` terminated with an error exit status (4) -- Execution is retried (1)
[be/3eff92] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX17709227_SRR21711856)` terminated with an error exit status (4) -- Execution is retried (1)
[8f/9abf84] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX17709228_SRR21711855)` terminated with an error exit status (4) -- Execution is retried (1)
[78/a0ac7c] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)` terminated with an error exit status (4) -- Execution is retried (2)
[df/f1c395] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9504942_SRR13055520)` terminated with an error exit status (4) -- Execution is retried (2)
[54/fb07ac] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)` terminated with an error exit status (4) -- Execution is retried (2)
[6e/9d170f] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9504942_SRR13055518)` terminated with an error exit status (4) -- Execution is retried (2)
[cf/8aa6ef] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9504942_SRR13055519)` terminated with an error exit status (4) -- Execution is retried (2)
[40/83ea1d] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9504942_SRR13055517)` terminated with an error exit status (4) -- Execution is retried (2)
[0f/963215] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX17709227_SRR21711856)` terminated with an error exit status (4) -- Execution is retried (2)
[ea/77963a] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)` terminated with an error exit status (4) -- Execution is retried (2)
[a1/405f94] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX17709228_SRR21711855)` terminated with an error exit status (4) -- Execution is retried (2)
[1a/154c02] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (DRX024467_DRR026872)` terminated with an error exit status (4) -- Execution is retried (2)
[d4/58f935] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9626017_SRR13191702)` terminated with an error exit status (4) -- Execution is retried (2)
ERROR ~ Error executing process > 'NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9504942_SRR13055520)'

Caused by:
  Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9504942_SRR13055520)` terminated with an error exit status (4)


Command executed:

  wget \
      -t 5 -nv -c -T 60 \
      -O SRX9504942_SRR13055520_1.fastq.gz \
      ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz
  
  echo "795d460abff6009c7f5ff7c14b773fbe  SRX9504942_SRR13055520_1.fastq.gz" > SRX9504942_SRR13055520_1.fastq.gz.md5
  md5sum -c SRX9504942_SRR13055520_1.fastq.gz.md5
  
  wget \
      -t 5 -nv -c -T 60 \
      -O SRX9504942_SRR13055520_2.fastq.gz \
      ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz
  
  echo "c3f34379356b28d6dac7212abc1a0a04  SRX9504942_SRR13055520_2.fastq.gz" > SRX9504942_SRR13055520_2.fastq.gz.md5
  md5sum -c SRX9504942_SRR13055520_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 /sw/rl9c/singularity/3.9.7/rl9_go1.19.4/install/var/singularity/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:
  /cluster/tmp/userx/data/work/d5/9a9851d83763d2de95a9e7d6a6d42c

Container:
  /cluster/tmp/userx/data/work/singularity/depot.galaxyproject.org-singularity-wget-1.20.1.img

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '.nextflow.log' file for details
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