search

nf-core / hic

Analysis of Chromosome Conformation Capture data (Hi-C)
https://nf-co.re/hic
MIT License
80 stars 55 forks source link

java error #180

Open AlcaArctica opened 9 months ago

AlcaArctica commented 9 months ago

Description of the bug

I am consistently getting a ominous java error with -profile singularity. I tried with different java versions openjdk 11.0.1 2018-10-16 LTS openjdk 17.0.8-internal 2023-07-18 openjdk 20.0.1 2023-04-18 but it doesnt seem to make a difference. The command and output are described below. I also tried -profile charliecloud, but here a different java error comes up:

ERROR ~ Error executing process > 'NFCORE_HIC:HIC:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (1)'
Caused by:
  java.nio.channels.OverlappingFileLockException

with -profile conda the workflow at least starts, so I know my sample sheet and the other parameters are functional. But then it quickly fails with 

[[id:Sample_1, single_end:false, chunk:0], [/lustre/projects/dazzlerAssembly/asm_mGlyDav/data/hic/L119399_Track-163672_R1.fastq.gz, /lustre/projects/dazzlerAssembly/asm_mGlyDav/data/hic/L119399_Track-163672_R2.fastq.gz]]
[[id:Sample_2, single_end:false, chunk:0], [/lustre/projects/dazzlerAssembly/asm_mGlyDav/data/hic/L119400_Track-163673_R1.fastq.gz, /lustre/projects/dazzlerAssembly/asm_mGlyDav/data/hic/L119400_Track-163673_R2.fastq.gz]]
[[id:Sample_3, single_end:false, chunk:0], [/lustre/projects/dazzlerAssembly/asm_mGlyDav/data/hic/L119401_Track-163720_R1.fastq.gz, /lustre/projects/dazzlerAssembly/asm_mGlyDav/data/hic/L119401_Track-163720_R2.fastq.gz]]
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 \
       \
      asm_mGlyDav.hap1.deepVariant.fasta.sizes \
      40000 > cooler_bins_40000.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 "/tmp/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/bin/cooler", line 6, in <module>
      from cooler.cli import cli
    File "/tmp/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/lib/python3.10/site-packages/cooler/__init__.py", line 14, in <module>
      from .api import Cooler, annotate
    File "/tmp/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/lib/python3.10/site-packages/cooler/api.py", line 13, in <module>
      from .core import (
    File "/tmp/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/lib/python3.10/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' (/tmp/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/lib/python3.10/site-packages/pandas/api/types/__init__.py)

Work dir:
  /tmp/24/4c78bfcda8b18319e8e1e21bd213bc

So three different error messages... I would really like to get -profile singularity to work, but have no idea on how to proceed. Could you point me in the right direction, please? Thank you very much.

Command used and terminal output

nextflow run nf-core/hic --input /lustre/projects/dazzlerAssembly/test_nf_hic/samplesheet.csv --outdir /lustre/projects/dazzlerAssembly/test_nf_hic/hic_results -profile singularity -w /tmp/ --fasta /lustre/projects/dazzlerAssembly/asm_mGlyDav/assembly/polishing/hap1/asm_mGlyDav.hap1.deepVariant.fasta --restriction_site '^GATC,G^ANTC,C^TNAG,T^TAA' --ligation_site 'GATCGATC,GATCANTC,GANTGATC,GANTANTC,GATCTNAG,GANTTNAG,CTNAGATC,CTNAANTC,TTAGATC,TTAANTC,TTATTNAG,GATCTAA,GANTTAA,CTNATAA,TTATAA,CTNATNAG'
N E X T F L O W  ~  version 23.04.2
Launching `https://github.com/nf-core/hic` [tiny_noether] DSL2 - revision: fe4ac65631 [master]

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/hic v2.1.0-gfe4ac65
------------------------------------------------------
Core Nextflow options
  revision                     : master
  runName                      : tiny_noether
  containerEngine              : singularity
  launchDir                    : /tmp
  workDir                      : /tmp
  projectDir                   : /home/uelze/.nextflow/assets/nf-core/hic
  userName                     : uelze
  profile                      : singularity
  configFiles                  : /home/uelze/.nextflow/assets/nf-core/hic/nextflow.config

Input/output options
  input                        : /lustre/projects/dazzlerAssembly/test_nf_hic/samplesheet.csv
  outdir                       : /lustre/projects/dazzlerAssembly/test_nf_hic/hic_results

Reference genome options
  fasta                        : /lustre/projects/dazzlerAssembly/asm_mGlyDav/assembly/polishing/hap1/asm_mGlyDav.hap1.deepVariant.fasta

Digestion Hi-C
  restriction_site             : ^GATC,G^ANTC,C^TNAG,T^TAA
  ligation_site                : GATCGATC,GATCANTC,GANTGATC,GANTANTC,GATCTNAG,GANTTNAG,CTNAGATC,CTNAANTC,TTAGATC,TTAANTC,TTATTNAG,GATCTAA,GANTTAA,CTNATAA,TTATAA,CTNATNAG

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
------------------------------------------------------
[-        ] process > NFCORE_HIC:HIC:INPUT_CHECK:SAMPLESHEET_CHECK               -
[-        ] process > NFCORE_HIC:HIC:INPUT_CHECK:SAMPLESHEET_CHECK               -
[-        ] process > NFCORE_HIC:HIC:PREPARE_GENOME:BOWTIE2_BUILD                -
[-        ] process > NFCORE_HIC:HIC:PREPARE_GENOME:CUSTOM_GETCHROMSIZES         -
[-        ] process > NFCORE_HIC:HIC:PREPARE_GENOME:GET_RESTRICTION_FRAGMENTS    -
[-        ] process > NFCORE_HIC:HIC:FASTQC                                      -
[-        ] 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                         -
[-        ] process > NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS                      -
[-        ] 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:INPUT_CHECK:SAMPLESHEET_CHECK'

Caused by:
  java.io.IOException: Function not implemented

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

Relevant files

No response

System information

No response

nservant commented 5 months ago

Hi, I'm afraid the error is not related to the nf-core-hic pipeline itself, but more to the env or the config. Did you try to ask for help in the slack forum ?