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carpentries-incubator / workflows-nextflow

Workflow management with Nextflow and nf-core
https://carpentries-incubator.github.io/workflows-nextflow/
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Nextflow review @bobturneruk ep11, error script 6 #141

Open ggrimes opened 2 months ago

ggrimes commented 2 months ago

I get this error when running script6:

Error executing process > 'MULTIQC'

Caused by:
  Process `MULTIQC` terminated with an error exit status (1)

Command executed:

  multiqc .

Command exit status:
  1

Command output:
  Searching   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 141/141  

Command error:
             ^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/home/bobturner/miniconda3/envs/nf-training/lib/python3.12/site-packages/multiqc/utils/config.py", line 256, in update_dict
      if isinstance(val, collections.Mapping):
                         ^^^^^^^^^^^^^^^^^^^
  AttributeError: module 'collections' has no attribute 'Mapping'
  ============================================================
  [ERROR  ]         multiqc : Oops! The 'seqyclean' MultiQC module broke... 
    Please copy the following traceback and report it at https://github.com/ewels/MultiQC/issues 
    If possible, please include a log file that triggers the error - the last file found was:
      None
  ============================================================
  Module seqyclean raised an exception: Traceback (most recent call last):
    File "/home/bobturner/miniconda3/envs/nf-training/lib/python3.12/site-packages/multiqc/multiqc.py", line 594, in run
      output = mod()
               ^^^^^
    File "/home/bobturner/miniconda3/envs/nf-training/lib/python3.12/site-packages/multiqc/modules/seqyclean/seqyclean.py", line 18, in __init__
      super(MultiqcModule, self).__init__(
    File "/home/bobturner/miniconda3/envs/nf-training/lib/python3.12/site-packages/multiqc/modules/base_module.py", line 45, in __init__
      config.update({anchor: mod_cust_config.get("custom_config", {})})
    File "/home/bobturner/miniconda3/envs/nf-training/lib/python3.12/site-packages/multiqc/utils/config.py", line 250, in update
      return update_dict(globals(), u)
             ^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/home/bobturner/miniconda3/envs/nf-training/lib/python3.12/site-packages/multiqc/utils/config.py", line 256, in update_dict
      if isinstance(val, collections.Mapping):
                         ^^^^^^^^^^^^^^^^^^^
  AttributeError: module 'collections' has no attribute 'Mapping'
  ============================================================
  [ERROR  ]         multiqc : Oops! The 'optitype' MultiQC module broke... 
    Please copy the following traceback and report it at https://github.com/ewels/MultiQC/issues 
    If possible, please include a log file that triggers the error - the last file found was:
      None
  ============================================================
  Module optitype raised an exception: Traceback (most recent call last):
    File "/home/bobturner/miniconda3/envs/nf-training/lib/python3.12/site-packages/multiqc/multiqc.py", line 594, in run
      output = mod()
               ^^^^^
    File "/home/bobturner/miniconda3/envs/nf-training/lib/python3.12/site-packages/multiqc/modules/optitype/optitype.py", line 24, in __init__
      super(MultiqcModule, self).__init__(
    File "/home/bobturner/miniconda3/envs/nf-training/lib/python3.12/site-packages/multiqc/modules/base_module.py", line 45, in __init__
      config.update({anchor: mod_cust_config.get("custom_config", {})})
    File "/home/bobturner/miniconda3/envs/nf-training/lib/python3.12/site-packages/multiqc/utils/config.py", line 250, in update
      return update_dict(globals(), u)
             ^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/home/bobturner/miniconda3/envs/nf-training/lib/python3.12/site-packages/multiqc/utils/config.py", line 256, in update_dict
      if isinstance(val, collections.Mapping):
                         ^^^^^^^^^^^^^^^^^^^
  AttributeError: module 'collections' has no attribute 'Mapping'
  ============================================================
  [WARNING]         multiqc : No analysis results found. Cleaning up..
  [INFO   ]         multiqc : MultiQC complete

Work dir:
  /home/bobturner/nf-training/work/13/2a6ef5a3e567c3f56e41d67eefe205

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