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Does anyone have trouble even running the test dat...
# fetchngs
m
Does anyone have trouble even running the test data for this pipeline? I just tried it and I keep getting this error (see thread for details)
Command executed:
Copy code
nextflow run nf-core/fetchngs -r 1.12.0 -c nextflow.config -profile singularity,test --outdir results_fetchngs
Output (truncated):
Copy code
[f1/745bdc] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX2370468_SRR5048077)` terminated with an error exit status (4) -- Execution is retried (1)
[a0/3767ac] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX2370491_SRR5048100)` terminated with an error exit status (4) -- Execution is retried (1)
[ca/868e96] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX1603392_SRR3192408)` terminated with an error exit status (4) -- Execution is retried (1)
[ea/63ed18] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX1603630_SRR3192658)` terminated with an error exit status (4) -- Execution is retried (1)
[e7/3aeded] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX2370490_SRR5048099)` terminated with an error exit status (4) -- Execution is retried (1)
[8b/c583f3] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX1603393_SRR3192409)` terminated with an error exit status (4) -- Execution is retried (1)
[74/279ab7] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX1603629_SRR3192657)` terminated with an error exit status (4) -- Execution is retried (1)
[e8/6a253f] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX2370469_SRR5048078)` terminated with an error exit status (4) -- Execution is retried (1)
[c7/87c645] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX2370468_SRR5048077)` terminated with an error exit status (4) -- Execution is retried (2)
[82/cb253a] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX2370491_SRR5048100)` terminated with an error exit status (4) -- Execution is retried (2)
[f3/34b1e2] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX1603392_SRR3192408)` terminated with an error exit status (4) -- Execution is retried (2)
[06/be5ecc] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX1603630_SRR3192658)` terminated with an error exit status (4) -- Execution is retried (2)
[05/1cbc88] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX2370490_SRR5048099)` terminated with an error exit status (4) -- Execution is retried (2)
[64/a4b6bb] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX1603393_SRR3192409)` terminated with an error exit status (4) -- Execution is retried (2)
[fd/6566e9] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX1603629_SRR3192657)` terminated with an error exit status (4) -- Execution is retried (2)
[39/baf2e2] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX2370469_SRR5048078)` terminated with an error exit status (4) -- Execution is retried (2)
ERROR ~ Error executing process > 'NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX2370468_SRR5048077)'

Caused by:
  Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX2370468_SRR5048077)` terminated with an error exit status (4)


Command executed:

  wget \
      -t 5 -nv -c -T 60 \
      -O SRX2370468_SRR5048077_1.fastq.gz \
      <http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR504/007/SRR5048077/SRR5048077_1.fastq.gz|ftp.sra.ebi.ac.uk/vol1/fastq/SRR504/007/SRR5048077/SRR5048077_1.fastq.gz>

  echo "6beb20b2cd99542433986b8fe844ef09  SRX2370468_SRR5048077_1.fastq.gz" > SRX2370468_SRR5048077_1.fastq.gz.md5
  md5sum -c SRX2370468_SRR5048077_1.fastq.gz.md5

  wget \
      -t 5 -nv -c -T 60 \
      -O SRX2370468_SRR5048077_2.fastq.gz \
      <http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR504/007/SRR5048077/SRR5048077_2.fastq.gz|ftp.sra.ebi.ac.uk/vol1/fastq/SRR504/007/SRR5048077/SRR5048077_2.fastq.gz>

  echo "4f63ef9e16dc9f0f8be159b02d40f0c6  SRX2370468_SRR5048077_2.fastq.gz" > SRX2370468_SRR5048077_2.fastq.gz.md5
  md5sum -c SRX2370468_SRR5048077_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:
  INFO:    Converting SIF file to temporary sandbox...
  WARNING: Skipping mount /ibex/user/pampum/2024-08-29_nextflow-test/env/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
executor >  slurm (34)
[d9/82c874] NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRX1603629)                                          [100%] 8 of 8 ✔
[f7/4f24e3] NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (4)                                                   [100%] 8 of 8 ✔
[84/a03121] NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX2370491_SRR5048100)                                    [ 75%] 18 of 24, failed: 18, retries: 16
[-        ] NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:CUSTOM_SRATOOLSNCBISETTINGS -
[-        ] NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH           -
[-        ] NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP        -
[-        ] NFCORE_FETCHNGS:SRA:ASPERA_CLI                                                               -
[-        ] NFCORE_FETCHNGS:SRA:SRA_TO_SAMPLESHEET                                                       -
[-        ] NFCORE_FETCHNGS:SRA:MULTIQC_MAPPINGS_CONFIG                                                  -
[f1/745bdc] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX2370468_SRR5048077)` terminated with an error exit status (4) -- Execution is retried (1)
[a0/3767ac] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX2370491_SRR5048100)` terminated with an error exit status (4) -- Execution is retried (1)
[ca/868e96] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX1603392_SRR3192408)` terminated with an error exit status (4) -- Execution is retried (1)
[ea/63ed18] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX1603630_SRR3192658)` terminated with an error exit status (4) -- Execution is retried (1)
[e7/3aeded] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX2370490_SRR5048099)` terminated with an error exit status (4) -- Execution is retried (1)
[8b/c583f3] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX1603393_SRR3192409)` terminated with an error exit status (4) -- Execution is retried (1)
[74/279ab7] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX1603629_SRR3192657)` terminated with an error exit status (4) -- Execution is retried (1)
[e8/6a253f] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX2370469_SRR5048078)` terminated with an error exit status (4) -- Execution is retried (1)
[c7/87c645] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX2370468_SRR5048077)` terminated with an error exit status (4) -- Execution is retried (2)
[82/cb253a] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX2370491_SRR5048100)` terminated with an error exit status (4) -- Execution is retried (2)
[f3/34b1e2] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX1603392_SRR3192408)` terminated with an error exit status (4) -- Execution is retried (2)
[06/be5ecc] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX1603630_SRR3192658)` terminated with an error exit status (4) -- Execution is retried (2)
[05/1cbc88] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX2370490_SRR5048099)` terminated with an error exit status (4) -- Execution is retried (2)
[64/a4b6bb] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX1603393_SRR3192409)` terminated with an error exit status (4) -- Execution is retried (2)
[fd/6566e9] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX1603629_SRR3192657)` terminated with an error exit status (4) -- Execution is retried (2)
[39/baf2e2] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX2370469_SRR5048078)` terminated with an error exit status (4) -- Execution is retried (2)
ERROR ~ Error executing process > 'NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX2370468_SRR5048077)'

Caused by:
  Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX2370468_SRR5048077)` terminated with an error exit status (4)


Command executed:

  wget \
      -t 5 -nv -c -T 60 \
      -O SRX2370468_SRR5048077_1.fastq.gz \
      <http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR504/007/SRR5048077/SRR5048077_1.fastq.gz|ftp.sra.ebi.ac.uk/vol1/fastq/SRR504/007/SRR5048077/SRR5048077_1.fastq.gz>

  echo "6beb20b2cd99542433986b8fe844ef09  SRX2370468_SRR5048077_1.fastq.gz" > SRX2370468_SRR5048077_1.fastq.gz.md5
  md5sum -c SRX2370468_SRR5048077_1.fastq.gz.md5

  wget \
      -t 5 -nv -c -T 60 \
      -O SRX2370468_SRR5048077_2.fastq.gz \
      <http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR504/007/SRR5048077/SRR5048077_2.fastq.gz|ftp.sra.ebi.ac.uk/vol1/fastq/SRR504/007/SRR5048077/SRR5048077_2.fastq.gz>

  echo "4f63ef9e16dc9f0f8be159b02d40f0c6  SRX2370468_SRR5048077_2.fastq.gz" > SRX2370468_SRR5048077_2.fastq.gz.md5
  md5sum -c SRX2370468_SRR5048077_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:
  INFO:    Converting SIF file to temporary sandbox...
  WARNING: Skipping mount /ibex/user/pampum/2024-08-29_nextflow-test/env/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>'
  INFO:    Cleaning up image...

Work dir:
  /ibex/user/pampum/2024-08-29_nextflow-test/work/43/e44afd86dff87e99a8e9b91cea52d3

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
d
Perhaps try using dev? See if it's the same issue I faced previously..
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