NFCORE_HIC:HIC:CUSTOM_DUMPSOFTWAREVERSIONS (1) terminated with an error exit status (1)

[aghr]

Description of the bug

The job CUSTOM_DUMPSOFTWAREVERSIONS should process software versions from file collated_versions.yml. I believe this file collated_versions.yml is created in some previous job of this pipeline. The creation of the file collated_versions.yml seems to have a bug as the resulting file collated_versions.yml does not agree to the YAML format, here is the excerpt that causes the error:

...
"NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:COMBINE_MATES":
python: 3.9.12
"NFCORE_HIC:HIC:TADS:COOLTOOLS_INSULATION":
cooltools: Matplotlib created a temporary config/cache directory at /tmp/matplotlib-wano91yj because the default path (/home/XXXX/.cache/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
0.5.1
"NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN_TRIMMED":
bowtie2: 2.4.4
samtools: 1.16.1
pigz: 2.6

...

To avoid that error I've tried to set the env var MPLCONFIGDIR but without success. I believe the reason is that env vars I define before running nf-core hic will not be defined inside the singularity container where the pipeline jobs are executed. Therein in these containers the env var MPLCONFIGDIR is still undefined.

I think the creation of the file collated_versions.yml needs to be improved to avoid copying warnings and other stuff from the output of 'software x --version' into the file collated_versions.yml .

Command used and terminal output

export MPLCONFIGDIR=/scratch/XXXX/nf_core_hic/matplotlib_config_dir
export NXF_SINGULARITY_CACHEDIR=/scratch/singularity_cache

nextflow run nf-core/hic -profile test,singularity --outdir /scratch/XXXX/nf_core_hic/output


===================
-[nf-core/hic] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_HIC:HIC:CUSTOM_DUMPSOFTWAREVERSIONS (1)'

Caused by:
  Process `NFCORE_HIC:HIC:CUSTOM_DUMPSOFTWAREVERSIONS (1)` terminated with an error exit status (1)

Command executed [/home/XXXX/.nextflow/agohrssets/nf-core/hic/./workflows/../modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwa
reversions.py]:

  #!/usr/bin/env python
  
  
  """Provide functions to merge multiple versions.yml files."""
  
  
  import yaml
  import platform
  from textwrap import dedent
  
  
  def _make_versions_html(versions):
      """Generate a tabular HTML output of all versions for MultiQC."""
      html = [
          dedent(
              """\
              <style>
              #nf-core-versions tbody:nth-child(even) {
                  background-color: #f2f2f2;
              }
              </style>
              <table class="table" style="width:100%" id="nf-core-versions">
                  <thead>
                      <tr>
                         <th> Process Name </th>
                          <th> Software </th>
                          <th> Version  </th>
                      </tr>
                  </thead>
              """
          )
      ]
      for process, tmp_versions in sorted(versions.items()):
          html.append("<tbody>")
          for i, (tool, version) in enumerate(sorted(tmp_versions.items())):
              html.append(
                  dedent(
                      f"""\
                      <tr>
                          <td><samp>{process if (i == 0) else ''}</samp></td>
                          <td><samp>{tool}</samp></td>
                          <td><samp>{version}</samp></td>
                      </tr>
                      """
                  )
              )
          html.append("</tbody>")
      html.append("</table>")
      return "\n".join(html)
  
  
  def main():
      """Load all version files and generate merged output."""
      versions_this_module = {}
      versions_this_module["NFCORE_HIC:HIC:CUSTOM_DUMPSOFTWAREVERSIONS"] = {
          "python": platform.python_version(),
          "yaml": yaml.__version__,
      }
  
      with open("collated_versions.yml") as f:
          versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
  
      # aggregate versions by the module name (derived from fully-qualified process name)
      versions_by_module = {}
      for process, process_versions in versions_by_process.items():
          module = process.split(":")[-1]
          try:
              if versions_by_module[module] != process_versions:
                  raise AssertionError(
                      "We assume that software versions are the same between all modules. "
                      "If you see this error-message it means you discovered an edge-case "
                      "and should open an issue in nf-core/tools. "
                  )
          except KeyError:
              versions_by_module[module] = process_versions
  
      versions_by_module["Workflow"] = {
          "Nextflow": "23.04.3",
          "nf-core/hic": "2.1.0",
      }
  
      versions_mqc = {
          "id": "software_versions",
          "section_name": "nf-core/hic Software Versions",
          "section_href": "https://github.com/nf-core/hic",
          "plot_type": "html",
          "description": "are collected at run time from the software output.",
          "data": _make_versions_html(versions_by_module),
      }
  
      with open("software_versions.yml", "w") as f:
          yaml.dump(versions_by_module, f, default_flow_style=False)
      with open("software_versions_mqc.yml", "w") as f:
          yaml.dump(versions_mqc, f, default_flow_style=False)
  
      with open("versions.yml", "w") as f:
          yaml.dump(versions_this_module, f, default_flow_style=False)
  
  
  if __name__ == "__main__":
      main()

Command exit status:
  1

Command output:
  (empty)

Command error:
  Traceback (most recent call last):
    File ".command.sh", line 101, in <module>
      main()
    File ".command.sh", line 61, in main
      versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/yaml/__init__.py", line 81, in load
      return loader.get_single_data()
             ^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/yaml/constructor.py", line 49, in get_single_data
      node = self.get_single_node()
             ^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/yaml/composer.py", line 36, in get_single_node
      document = self.compose_document()
                 ^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/yaml/composer.py", line 55, in compose_document
      node = self.compose_node(None, None)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/yaml/composer.py", line 84, in compose_node
      node = self.compose_mapping_node(anchor)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/yaml/composer.py", line 133, in compose_mapping_node
      item_value = self.compose_node(node, item_key)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/yaml/composer.py", line 84, in compose_node
      node = self.compose_mapping_node(anchor)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/yaml/composer.py", line 127, in compose_mapping_node
      while not self.check_event(MappingEndEvent):
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/yaml/parser.py", line 98, in check_event
      self.current_event = self.state()
                           ^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/yaml/parser.py", line 428, in parse_block_mapping_key
      if self.check_token(KeyToken):
         ^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/yaml/scanner.py", line 115, in check_token
      while self.need_more_tokens():
            ^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/yaml/scanner.py", line 152, in need_more_tokens
      self.stale_possible_simple_keys()
    File "/usr/local/lib/python3.11/site-packages/yaml/scanner.py", line 291, in stale_possible_simple_keys
      raise ScannerError("while scanning a simple key", key.mark,
  yaml.scanner.ScannerError: while scanning a simple key
    in "collated_versions.yml", line 15, column 1
  could not find expected ':'
    in "collated_versions.yml", line 16, column 1

Work dir:
  /scratch/XXXX/nf_core_hic/work/e0/cfebcb3608555b7094944e8079bc42

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

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

Relevant files

nextflow.log

System information

• N E X T F L O W, version 23.04.3 build 5875
• compute server with Linux
• run on local hard disk of compute server
• run without slurm etc; local executor
• run with singularity version 3.8.6
• openjdk 17.0.3-internal 2022-04-19
• OpenJDK Runtime Environment (build 17.0.3-internal+0-adhoc..src)
• OpenJDK 64-Bit Server VM (build 17.0.3-internal+0-adhoc..src, mixed mode, sharing)
• NAME="CentOS Linux"
  • VERSION="7 (Core)"
  • ID="centos"
  • ID_LIKE="rhel fedora"
  • VERSION_ID="7"
  • PRETTY_NAME="CentOS Linux 7 (Core)"
  • ANSI_COLOR="0;31"
  • CPE_NAME="cpe:/o:centos:centos:7"

[edmundmiller]

Not sure why it's happening, probably just needs to be bumped to the latest versions.

[joey0214]

Hi, I have exactly the same error on the Bianca server from UPPMAX. anyway to skip this step?

[edmundmiller]

Just in a config file and use nextflow -c bonus.config

process {
    withName: "CUSTOM_DUMPSOFTWAREVERSIONS" {
        ext.when = false
    }
}

[joey0214]

Thanks. it works after updated the config file