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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:
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 23.04.2Launching `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.configInput/output options input : /lustre/projects/dazzlerAssembly/test_nf_hic/samplesheet.csv outdir : /lustre/projects/dazzlerAssembly/test_nf_hic/hic_resultsReference genome options fasta : /lustre/projects/dazzlerAssembly/asm_mGlyDav/assembly/polishing/hap1/asm_mGlyDav.hap1.deepVariant.fastaDigestion 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,CTNATNAGDNAse Hi-C min_cis_dist : 0Alignments 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 --reorderValid Pairs Detection max_insert_size : 0 min_insert_size : 0 max_restriction_fragment_size: 0 min_restriction_fragment_size: 0Contact maps bin_size : 1000000 ice_filter_high_count_perc : 0 res_zoomify : nullDownstream 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
The text was updated successfully, but these errors were encountered:
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 ?
Description of the bug
I am consistently getting a ominous java error with
-profile singularity
. I tried with different java versionsopenjdk 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: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 withSo 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
Relevant files
No response
System information
No response
The text was updated successfully, but these errors were encountered: