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nf-core / cutandrun

Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
https://nf-co.re/cutandrun
MIT License
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Error executing process > 'NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_QC:DEEPTOOLS_MULTIBAMSUMMARY (all_target_bams)': AttributeError: module 'matplotlib.cm' has no attribute 'register_cmap' #251

Open haipinghao opened 3 months ago

haipinghao commented 3 months ago

Description of the bug

I ran "nextflow run nf-core/cutandrun -profile test,conda" command after installing conda and nextflow following the instruction and got the error message

Command used and terminal output

$ nextflow run nf-core/cutandrun -profile test,conda
-[nf-core/cutandrun] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_QC:DEEPTOOLS_MULTIBAMSUMMARY (all_target_bams)'

Caused by:
  Process `NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_QC:DEEPTOOLS_MULTIBAMSUMMARY (all_target_bams)` terminated with an error exit status (1)

Command executed:

  multiBamSummary bins \
      --smartLabels --binSize 500 \
      --labels h3k27me3_R1 igg_ctrl_R1 \
      --bamfiles h3k27me3_R1.target.linear_dedup.sorted.bam igg_ctrl_R1.target.linear_dedup.sorted.bam \
      --numberOfProcessors 2 \
      --outFileName all_bam.bamSummary.npz

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_QC:DEEPTOOLS_MULTIBAMSUMMARY":
      deeptools: $(multiBamSummary --version | sed -e "s/multiBamSummary //g")
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  Traceback (most recent call last):
    File "/NGS_Core/CutAndRun/work/conda/env-0d01150023c68e439ebff3eb959d98bf/bin/multiBamSummary", line 5, in <module>
      from deeptools.multiBamSummary import main
    File "/NGS_Core/CutAndRun/work/conda/env-0d01150023c68e439ebff3eb959d98bf/lib/python3.11/site-packages/deeptools/multiBamSummary.py", line 9, in <module>
      import deeptools.countReadsPerBin as countR
    File "/NGS_Core/CutAndRun/work/conda/env-0d01150023c68e439ebff3eb959d98bf/lib/python3.11/site-packages/deeptools/countReadsPerBin.py", line 9, in <module>
      import deeptools.utilities
    File "/NGS_Core/CutAndRun/work/conda/env-0d01150023c68e439ebff3eb959d98bf/lib/python3.11/site-packages/deeptools/utilities.py", line 7, in <module>
      from deeptools import cm  # noqa: F401
      ^^^^^^^^^^^^^^^^^^^^^^^^
    File "/NGS_Core/CutAndRun/work/conda/env-0d01150023c68e439ebff3eb959d98bf/lib/python3.11/site-packages/deeptools/cm.py", line 1087, in <module>
      mpl_cm.register_cmap(_name, _cmap)
      ^^^^^^^^^^^^^^^^^^^^
  AttributeError: module 'matplotlib.cm' has no attribute 'register_cmap'

Work dir:
  /NGS_Core/CutAndRun/work/df/50bbc2679a218fcccf7c49502a3ac4

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

Relevant files

No response

System information

Nextflow version 24.04.4 Hardware: multicore server Executor: none Container engine: Conda OS: Ubuntu Version of nf-core/cutandrun v3.2.2-g6e1125d

chris-cheshire commented 3 months ago

Looks like a cluster issue, is this still a problem?

haipinghao commented 3 months ago

Thank you for your response. No, this is no longer an issue.

On Thu, Aug 29, 2024 at 2:20 AM Chris Cheshire @.***> wrote:

Looks like a cluster issue, is this still a problem?

— Reply to this email directly, view it on GitHub https://github.com/nf-core/cutandrun/issues/251#issuecomment-2316887738, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASRHGIHKEKWS3GEU55OXQCTZT3DUZAVCNFSM6AAAAABMERCJKSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMJWHA4DONZTHA . You are receiving this because you authored the thread.Message ID: @.***>