Hi I'm running the hic test pipeline. Any tips for...
# hic
k
Hi I'm running the hic test pipeline. Any tips for troubleshooting "ImportError: cannot import name 'is_categorical' from 'pandas.api.types' " ?
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nextflow run nf-core/hic -profile test,conda --outdir /home/floer/nf_test                                                    executor >  local (7)
[47/557dd9] NFCORE_HIC:HIC:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)                      [100%] 1 of 1 ✔
[bc/3b6050] NFCORE_HIC:HIC:PREPARE_GENOME:BOWTIE2_BUILD (W303_SGD_2015_JRIU00000000.fsa)        [100%] 1 of 1 ✔
[f4/a8e314] NFCORE_HIC:HIC:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (W303_SGD_2015_JRIU00000000.fsa) [100%] 1 of 1 ✔
[2a/cafb8d] NFCORE_HIC:HIC:PREPARE_GENOME:GET_RESTRICTION_FRAGMENTS (A^AGCTT)                   [100%] 1 of 1 ✔
[a6/cba38e] NFCORE_HIC:HIC:FASTQC (SRR4292758)                                                  [100%] 1 of 1 ✔
[-        ] NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN                                  -
[-        ] NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:TRIM_READS                                     -
[-        ] NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN_TRIMMED                          -
[-        ] NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:MERGE_BOWTIE2                                  -
[-        ] NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:COMBINE_MATES                                  -
[-        ] NFCORE_HIC:HIC:HICPRO:GET_VALID_INTERACTION                                         -
[-        ] NFCORE_HIC:HIC:HICPRO:MERGE_VALID_INTERACTION                                       -
[-        ] NFCORE_HIC:HIC:HICPRO:MERGE_STATS                                                   -
[-        ] NFCORE_HIC:HIC:HICPRO:HICPRO2PAIRS                                                  -
[cc/0c1892] NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS (null})                                       [100%] 2 of 2, failed: 2 ✘
[-        ] NFCORE_HIC:HIC:COOLER:COOLER_CLOAD                                                  -
[-        ] NFCORE_HIC:HIC:COOLER:COOLER_BALANCE                                                -
[-        ] NFCORE_HIC:HIC:COOLER:COOLER_ZOOMIFY                                                -
[-        ] NFCORE_HIC:HIC:COOLER:COOLER_DUMP                                                   -
[-        ] NFCORE_HIC:HIC:COOLER:SPLIT_COOLER_DUMP                                             -
[-        ] NFCORE_HIC:HIC:HIC_PLOT_DIST_VS_COUNTS                                              -
[-        ] NFCORE_HIC:HIC:COMPARTMENTS:COOLTOOLS_EIGSCIS                                       -
[-        ] NFCORE_HIC:HIC:TADS:COOLTOOLS_INSULATION                                            -
[-        ] NFCORE_HIC:HIC:TADS:HIC_FIND_TADS                                                   -
[-        ] NFCORE_HIC:HIC:CUSTOM_DUMPSOFTWAREVERSIONS                                          -
[-        ] NFCORE_HIC:HIC:MULTIQC                                                              -
Execution cancelled -- Finishing pending tasks before exit

ERROR ~ Error executing process > 'NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS (null})'

Caused by:
  Process `NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS (null})` terminated with an error exit status (1)


Command executed:

  cooler makebins \
       \
      W303_SGD_2015_JRIU00000000.fsa.sizes \
      2000 > cooler_bins_2000.bed
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS":
      cooler: $(cooler --version 2>&1 | sed 's/cooler, version //')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  Traceback (most recent call last):
    File "/home/floer/work/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/bin/cooler", line 6, in <module>
      from cooler.cli import cli
    File "/home/floer/work/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/lib/python3.11/site-packages/cooler/__init__.py", line 14, in <module>
      from .api import Cooler, annotate
    File "/home/floer/work/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/lib/python3.11/site-packages/cooler/api.py", line 13, in <module>
      from .core import (
    File "/home/floer/work/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/lib/python3.11/site-packages/cooler/core.py", line 3, in <module>
      from pandas.api.types import is_categorical
  ImportError: cannot import name 'is_categorical' from 'pandas.api.types' (/home/floer/work/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/lib/python3.11/site-packages/pandas/api/types/__init__.py)

Work dir:
  /home/floer/work/0f/27c3e96b6a4de722b1cdd73e386a1a

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '.nextflow.log' file for details
s
Are you able to try with docker or singularity/apptainer instead of conda?