ERROR ~ Error executing process > 'NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS (null})'
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Description
Description of the bug
Hi, I tried to run the nextflow for my HiC analysis, however, I found I constantly run into the issue with mcool even I tried to --skip_mcool.
I use the -profile conda for this run
Command used and terminal output
nextflow run nf-core/hic \
-profile conda \
--input /data/zxt/2025_CUTRUN/1c_MDSO/sample.csv \
--fasta /data/genome-ref/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa \
--bwt2_index /data/genome-ref/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/ \
--chromosome_size /data/genome-ref/Homo_sapiens/UCSC/hg38/Annotation/hg38.chrom.sizes \
--skip_mcool \
--skip_compartments \
--skip_tads \
--skip_maps \
--dnase \
--outdir results/
curl: (35) Recv failure: Connection reset by peer
N E X T F L O W ~ version 23.10.1
Launching `https://github.com/nf-core/hic` [peaceful_waddington] DSL2 - revision: fe4ac65631 [master]
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,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/hic v2.1.0-gfe4ac65
------------------------------------------------------
Core Nextflow options
revision : master
runName : peaceful_waddington
launchDir : /data/zxt/2025_CUTRUN/1c_MDSO
workDir : /data/zxt/2025_CUTRUN/1c_MDSO/work
projectDir : /home/srv-xzhang38/.nextflow/assets/nf-core/hic
userName : srv-xzhang38
profile : conda
configFiles : /home/srv-xzhang38/.nextflow/assets/nf-core/hic/nextflow.config
Input/output options
input : /data/zxt/2025_CUTRUN/1c_MDSO/sample.csv
outdir : results/
Reference genome options
fasta : /data/genome-ref/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa
bwt2_index : /data/genome-ref/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/
Digestion Hi-C
chromosome_size : /data/genome-ref/Homo_sapiens/UCSC/hg38/Annotation/hg38.chrom.sizes
DNAse Hi-C
dnase : true
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
Skip options
skip_maps : true
skip_tads : true
skip_compartments : true
skip_mcool : true
!! 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
------------------------------------------------------
executor > local (3)
executor > local (4)
executor > local (4)
[12/e8399a] process > NFCORE_HIC:HIC:INPUT_CHECK:SAMPLESHEET_CHECK (sample.csv) [100%] 1 of 1 ✔
[59/a3ce31] process > NFCORE_HIC:HIC:FASTQC (1c_DMSO) [ 0%] 0 of 1
[- ] process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN -
[- ] process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:MAPPING_STATS_DNASE -
[- ] process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:COMBINE_MATES -
[- ] process > NFCORE_HIC:HIC:HICPRO:GET_VALID_INTERACTION_DNASE -
[- ] process > NFCORE_HIC:HIC:HICPRO:MERGE_VALID_INTERACTION -
[- ] process > NFCORE_HIC:HIC:HICPRO:MERGE_STATS -
[- ] process > NFCORE_HIC:HIC:HICPRO:HICPRO2PAIRS -
[46/87ae01] process > NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS (null}) [ 0%] 0 of 2
[- ] 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:CUSTOM_DUMPSOFTWAREVERSIONS -
[- ] process > NFCORE_HIC:HIC:MULTIQC -
[[id:1c_DMSO, single_end:false, chunk:0], [/data/zxt/2025_CUTRUN/1c_MDSO/ic_DMSO_R1.fastq.gz, /data/zxt/2025_CUTRUN/1c_MDSO/ic_DMSO_R2.fastq.gz]]
Creating env using conda: bioconda::bowtie2=2.4.4 bioconda::samtools=1.16.1 conda-forge::pigz=2.6 [cache /data/zxt/2025_CUTRUN/1c_MDSO/work/conda/env-0477d8fd416f3ca1d039a20e7ade196f]
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 \
\
hg38.chrom.sizes \
250000 > cooler_bins_250000.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:
executor > local (4)
[12/e8399a] process > NFCORE_HIC:HIC:INPUT_CHECK:SAMPLESHEET_CHECK (sample.csv) [100%] 1 of 1 ✔
[59/a3ce31] process > NFCORE_HIC:HIC:FASTQC (1c_DMSO) [ 0%] 0 of 1
[- ] process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN -
[- ] process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:MAPPING_STATS_DNASE -
[- ] process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:COMBINE_MATES -
[- ] process > NFCORE_HIC:HIC:HICPRO:GET_VALID_INTERACTION_DNASE -
[- ] process > NFCORE_HIC:HIC:HICPRO:MERGE_VALID_INTERACTION -
[- ] process > NFCORE_HIC:HIC:HICPRO:MERGE_STATS -
[- ] process > NFCORE_HIC:HIC:HICPRO:HICPRO2PAIRS -
[ba/256d59] process > NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS (null}) [100%] 2 of 2, failed: 2 ✘
[- ] 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:CUSTOM_DUMPSOFTWAREVERSIONS -
[- ] process > NFCORE_HIC:HIC:MULTIQC -
[[id:1c_DMSO, single_end:false, chunk:0], [/data/zxt/2025_CUTRUN/1c_MDSO/ic_DMSO_R1.fastq.gz, /data/zxt/2025_CUTRUN/1c_MDSO/ic_DMSO_R2.fastq.gz]]
Creating env using conda: bioconda::bowtie2=2.4.4 bioconda::samtools=1.16.1 conda-forge::pigz=2.6 [cache /data/zxt/2025_CUTRUN/1c_MDSO/work/conda/env-0477d8fd416f3ca1d039a20e7ade196f]
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 \
\
hg38.chrom.sizes \
250000 > cooler_bins_250000.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:
executor > local (4)
[12/e8399a] process > NFCORE_HIC:HIC:INPUT_CHECK:SAMPLESHEET_CHECK (sample.csv) [100%] 1 of 1 ✔
[59/a3ce31] process > NFCORE_HIC:HIC:FASTQC (1c_DMSO) [ 0%] 0 of 1
[- ] process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN [ 0%] 0 of 2
[- ] process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:MAPPING_STATS_DNASE -
[- ] process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:COMBINE_MATES -
[- ] process > NFCORE_HIC:HIC:HICPRO:GET_VALID_INTERACTION_DNASE -
[- ] process > NFCORE_HIC:HIC:HICPRO:MERGE_VALID_INTERACTION -
[- ] process > NFCORE_HIC:HIC:HICPRO:MERGE_STATS -
[- ] process > NFCORE_HIC:HIC:HICPRO:HICPRO2PAIRS -
[ba/256d59] process > NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS (null}) [100%] 2 of 2, failed: 2 ✘
[- ] 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: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 (1)
Command executed:
cooler makebins \
\
hg38.chrom.sizes \
250000 > cooler_bins_250000.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 "/data/zxt/2025_CUTRUN/1c_MDSO/work/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/bin/cooler", line 6, in <module>
from cooler.cli import cli
File "/data/zxt/2025_CUTRUN/1c_MDSO/work/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/lib/python3.11/site-packages/cooler/__init__.py", line 14, in <module>
from .api import Cooler, annotate
File "/data/zxt/2025_CUTRUN/1c_MDSO/work/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/lib/python3.11/site-packages/cooler/api.py", line 13, in <module>
from .core import (
File "/data/zxt/2025_CUTRUN/1c_MDSO/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' (/data/zxt/2025_CUTRUN/1c_MDSO/work/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/lib/python3.11/site-packages/pandas/api/types/__init__.py)
Work dir:
/data/zxt/2025_CUTRUN/1c_MDSO/work/46/87ae01fb37e593674cf88a8881adae
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
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reproducing the supplied nf-core/hic command and inspect the COOLER_MAKEBINS work directory at work/46/87ae01fb37e593674cf88a8881adae and its .command.out file. Check .nextflow.log and the reported pandas/cooler import traceback to determine why the process runs despite --skip_mcool. Done means the pipeline completes this stage without the ImportError and the skip option behaves as expected.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, data
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100