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nf-core / hic

Analysis of Chromosome Conformation Capture data (Hi-C)
https://nf-co.re/hic
MIT License
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Process `NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS (null})` terminated with an error exit status (127) #203

Open panpap25 opened 1 month ago

panpap25 commented 1 month ago

Description of the bug

Hey! I am dealing with the following problem that you can see. Seems that something is wrong with a specific essential module (?). I would deeply appreciate any advice.

Command used and terminal output

ppapadopoulos@hibu:~$ /opt/bin/nextflow/nextflow run -work-dir ./ nf-core/hic -r 2.1.0 --input /data/ppapadopoulos/HiC_DKO_DIONYSIS_samples/newfile1.csv --outdir /data/ppapadopoulos/HiC_DKO_DIONYSIS_samples/sample1 --genome mm10 --digestion dpnii

 N E X T F L O W   ~  version 24.04.2

Launching `https://github.com/nf-core/hic` [confident_angela] DSL2 - revision: fe4ac65631 [2.1.0]

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/hic v2.1.0-gfe4ac65
------------------------------------------------------
Core Nextflow options
  revision                     : 2.1.0
  runName                      : confident_angela
  launchDir                    : /home/ppapadopoulos
  workDir                      : /home/ppapadopoulos
  projectDir                   : /home/ppapadopoulos/.nextflow/assets/nf-core/hic
  userName                     : ppapadopoulos
  profile                      : standard
  configFiles                  : /home/ppapadopoulos/.nextflow/assets/nf-core/hic/nextflow.config

Input/output options
  input                        : /data/ppapadopoulos/HiC_DKO_DIONYSIS_samples/newfile1.csv
  outdir                       : /data/ppapadopoulos/HiC_DKO_DIONYSIS_samples/sample1

Reference genome options
  genome                       : mm10
  fasta                        : s3://ngi-igenomes/igenomes/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa
  bwt2_index                   : s3://ngi-igenomes/igenomes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/

Digestion Hi-C
  digestion                    : dpnii

DNAse Hi-C
  min_cis_dist                 : 0

Alignments
  bwt2_opts_end2end            : --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder
  bwt2_opts_trimmed            : --very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder

Valid Pairs Detection
  max_insert_size              : 0
  min_insert_size              : 0
  max_restriction_fragment_size: 0
  min_restriction_fragment_size: 0

Contact maps
  bin_size                     : 1000000
  ice_filter_high_count_perc   : 0
  res_zoomify                  : null

Downstream Analysis
  res_dist_decay               : 250000
  tads_caller                  : insulation
  res_tads                     : 40000

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/hic for your analysis please cite:

* The pipeline
  https://doi.org/10.5281/zenodo.2669513

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/hic/blob/master/CITATIONS.md
------------------------------------------------------
WARN: [nf-core/hic] You are attempting to run the pipeline without any custom configuration!

This will be dependent on your local compute environment but can be achieved via one or more of the following:
   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`
   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`
   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`

Please refer to the quick start section and usage docs for the pipeline.

executor >  local (2)
executor >  local (2)
executor >  local (2)
executor >  local (7)
[2a/ec5bbe] process > NFCORE_HIC:HIC:INPUT_CHECK:SAMPLESHEET_CHECK (newfile1.csv)     [100%] 1 of 1 ✔
[20/f50db0] process > NFCORE_HIC:HIC:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome.fa)  [100%] 1 of 1 ✔
executor >  local (7)
[2a/ec5bbe] process > NFCORE_HIC:HIC:INPUT_CHECK:SAMPLESHEET_CHECK (newfile1.csv)     [100%] 1 of 1 ✔
[20/f50db0] process > NFCORE_HIC:HIC:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome.fa)  [100%] 1 of 1 ✔
[25/89a917] process > NFCORE_HIC:HIC:PREPARE_GENOME:GET_RESTRICTION_FRAGMENTS (^GATC) [  0%] 0 of 1
executor >  local (7)
[2a/ec5bbe] process > NFCORE_HIC:HIC:INPUT_CHECK:SAMPLESHEET_CHECK (newfile1.csv)     [100%] 1 of 1 ✔
[20/f50db0] process > NFCORE_HIC:HIC:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome.fa)  [100%] 1 of 1 ✔
[25/89a917] process > NFCORE_HIC:HIC:PREPARE_GENOME:GET_RESTRICTION_FRAGMENTS (^GATC) [100%] 1 of 1 ✔
[92/faa11e] process > NFCORE_HIC:HIC:FASTQC (DKO2_HIC_S24)                            [100%] 1 of 1 ✔
[-        ] process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN              -
[-        ] process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:TRIM_READS                 -
[-        ] process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN_TRIMMED      -
[-        ] process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:MERGE_BOWTIE2              -
[-        ] process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:COMBINE_MATES              -
[-        ] process > NFCORE_HIC:HIC:HICPRO:GET_VALID_INTERACTION                     -
[-        ] process > NFCORE_HIC:HIC:HICPRO:MERGE_VALID_INTERACTION                   -
[-        ] process > NFCORE_HIC:HIC:HICPRO:MERGE_STATS                               -
[-        ] process > NFCORE_HIC:HIC:HICPRO:HICPRO2PAIRS                              -
[fc/95de49] process > NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS (null})                   [100%] 3 of 3, failed: 3 ✘
[-        ] process > NFCORE_HIC:HIC:COOLER:COOLER_CLOAD                              -
[-        ] process > NFCORE_HIC:HIC:COOLER:COOLER_BALANCE                            -
[-        ] process > NFCORE_HIC:HIC:COOLER:COOLER_ZOOMIFY                            -
[-        ] process > NFCORE_HIC:HIC:COOLER:COOLER_DUMP                               -
[-        ] process > NFCORE_HIC:HIC:COOLER:SPLIT_COOLER_DUMP                         -
[-        ] process > NFCORE_HIC:HIC:HIC_PLOT_DIST_VS_COUNTS                          -
[-        ] process > NFCORE_HIC:HIC:COMPARTMENTS:COOLTOOLS_EIGSCIS                   -
[-        ] process > NFCORE_HIC:HIC:TADS:COOLTOOLS_INSULATION                        -
[-        ] process > NFCORE_HIC:HIC:CUSTOM_DUMPSOFTWAREVERSIONS                      -
[-        ] process > NFCORE_HIC:HIC:MULTIQC                                          -

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 (127)

Command executed:

  cooler makebins \
       \
      genome.fa.sizes \
      1000000 > cooler_bins_1000000.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:
  127

Command output:
  (empty)

Command error:
  .command.sh: line 2: cooler: command not found

Work dir:
  /home/ppapadopoulos/6e/ed3535fa63fb556305f8183f9ed299

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

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

Relevant files

No response

System information

No response

panapapa14 commented 6 days ago

Hi there! Are there really any ideas about the issue I am dealing with? After some time that I didn't try to run the algorithm, I have been facing the very same problem. I would appreciate any guidance!