Java heap space

[luciazifcakova]

Description of the bug

I get "Java heap space" error for any configuration of Nextflow versions even though I have added "NXF_OPTS='-Xms1g -Xmx4g'" to my .bashrc...

N E X T F L O W ~ version 22.04.5
Launching https://github.com/nf-core/hicar [voluminous_noyce] DSL2 - revision: 429087d [1.0.0]------------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-..--~'
|\ | |__ __ / / \ |__) |__ } { | \| | \__, \__/ | \ |___ \-.,--, .,.,'
nf-core/hicar v1.0.0

Core Nextflow options
revision : 1.0.0
runName : voluminous_noyce
containerEngine : singularity
launchDir : /flash/MillerU/S_lessoniana_hic_maps
workDir : /flash/MillerU/S_lessoniana_hic_maps/work
projectDir : /home/l/lucia-zifcakova/.nextflow/assets/nf-core/hicar
userName : lucia-zifcakova
profile : oist,
configFiles : /home/l/lucia-zifcakova/.nextflow/assets/nf-core/hicar/nextflow.configInput/output options
input : samples.csv
outdir : ./Reference genome options
fasta : /bucket/MillerU/Zifcakova/Dovetail_ika_genomes/Dovetail_annotated_v_3_01_2022/S_les_scaffolds_soft_masked/S_les_scaffolds.fa
bwa_index : /bucket/MillerU/Zifcakova/Dovetail_ika_genomes/Dovetail_annotated_v_3_01_2022/S_les_scaffolds_soft_masked/S_les_scaffolds.bwt
gff : /bucket/MillerU/Zifcakova/s_les_tomo_anot/tsebra4_renamed_2.gffMAPS peak calling options
maps_digest_file : null
peak_pair_block : 1E+8Options related to tracks, juicer_tools, and circos
juicer_tools_jar : https://github.com/aidenlab/Juicebox/releases/download/v2.13.06/juicer_tools_2.13.06.jarOther options not expose
enrichment_fdr : 0.05Institutional config options
config_profile_description: The Okinawa Institute of Science and Technology Graduate University (OIST) HPC cluster profile provided by nf-core/configs.
config_profile_contact : OISTs Bioinformatics User Group <BioinfoUgrp@oist.jp>
config_profile_url : https://github.com/nf-core/configs/blob/master/docs/oist.mdMax job request options
max_cpus : 128
max_memory : 500 GB
max_time : 3d 18h!! Only displaying parameters that differ from the pipeline defaults !!

If you use nf-core/hicar for your analysis please cite:* The pipeline
https://doi.org/10.5281/zenodo.5618247* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x* Software dependencies
https://github.com/nf-core/hicar/blob/master/CITATIONS.md

[- ] process > NFCORE_HICAR:HICAR:INPUT_CHECK:SAMPLESHEET_CHECK -
[- ] process > NFCORE_HICAR:HICAR:CHECKSUMS -
[- ] process > NFCORE_HICAR:HICAR:PREPARE_GENOME:GFFREAD -
[- ] process > NFCORE_HICAR:HICAR:PREPARE_GENOME:GTF2BED -
[- ] process > NFCORE_HICAR:HICAR:PREPARE_GENOME:CHROMSIZES -
Java heap space -- Check script '/home/l/lucia-zifcakova/.nextflow/assets/nf-core/hicar/./workflows/../subworkflows/local/preparegenome.nf' at line: 85 or see '.nextflow.log' file for more details

Command used and terminal output

#!/bin/bash
#SBATCH --job-name=S_less_hicar
#SBATCH --partition=compute
#SBATCH --time=3-0
#SBATCH --mem=250G
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=20
#SBATCH --mail-user=lucia.zifcakova@oist.jp
#SBATCH --mail-type=BEGIN,FAIL,END
#SBATCH --output=./S_less_hicar.out

ml bioinfo-ugrp-modules
ml DebianMed
ml singularity
ml nf-core

nextflow run nf-core/hicar -r dev --input samples.csv --outdir ./ --gff /bucket/MillerU/Zifcakova/s_les_tomo_anot/tsebra4_renamed_2.gff -profile oist, singularity --fasta /bucket/MillerU/Zifcakova/Dovetail_ika_genomes/Dovetail_annotated_v_3_01_2022/S_les_scaffolds_soft_masked/S_les_scaffolds.fa --bwa_index /bucket/MillerU/Zifcakova/Dovetail_ika_genomes/Dovetail_annotated_v_3_01_2022/S_les_scaffolds_soft_masked/S_les_scaffolds --skip_diff_analysis

Relevant files

No response

System information

Currently Loaded Modules:

1. bioinfo-ugrp-modules 2) DebianMed/12.0 3) singularity/3.5.2 4) java-jdk/14 5) Nextflow2/22.04.5 6) nf-core/2.13.1
   HPC, CentOS 8.X with the 4.XX version of the Linux kernel

[jianhong]

Try to add macs_gsize to your parameter list to avoid loading huge genome into the memory. And there is a typo in your script at -profile oist, singularity. Should be -profile oist,singularity

[luciazifcakova]

Dear Jianhong, thank you for the information, it helped. I actually have Omni-C data that were cut by DNAse I but it is not on the list of enzymes. Can I add my own enzyme to the pipeline somehow? Best wishes, Lucia

…

________________________________ From: JIANHONG OU ***@***.***> Sent: Monday, April 22, 2024 10:40 PM To: nf-core/hicar ***@***.***> Cc: Lucia Zifcakova ***@***.***>; Author ***@***.***> Subject: Re: [nf-core/hicar] Java heap space (Issue #108) Try to add macs_gsize to your parameter list to avoid loading huge genome into the memory. And there is a typo in your script at -profile oist, singularity. Should be -profile oist,singularity — Reply to this email directly, view it on GitHub<#108 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AWQLEWBNMHLFOGUYAX2P57LY6UHLTAVCNFSM6AAAAABF757ORSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANRZGQ3TMMBXG4>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[jianhong]

Could you please let me know the enzyme? I can add it. My apologies that I did not write full documentation for that.Best!Your sincerely,Jianhong OuOn Apr 26, 2024, at 5:05 AM, luciazifcakova ***@***.***> wrote: Dear Jianhong, thank you for the information, it helped. I actually have Omni-C data that were cut by DNAse I but it is not on the list of enzymes. Can I add my own enzyme to the pipeline somehow? Best wishes, Lucia

…

________________________________ From: JIANHONG OU ***@***.***> Sent: Monday, April 22, 2024 10:40 PM To: nf-core/hicar ***@***.***> Cc: Lucia Zifcakova ***@***.***>; Author ***@***.***> Subject: Re: [nf-core/hicar] Java heap space (Issue #108) Try to add macs_gsize to your parameter list to avoid loading huge genome into the memory. And there is a typo in your script at -profile oist, singularity. Should be -profile oist,singularity — Reply to this email directly, view it on GitHub<#108 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AWQLEWBNMHLFOGUYAX2P57LY6UHLTAVCNFSM6AAAAABF757ORSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANRZGQ3TMMBXG4>. You are receiving this because you authored the thread.Message ID: ***@***.***> —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you commented.Message ID: ***@***.***>

[luciazifcakova]

Dear Jianhong, Omni-C use this enzyme: DNase I, a sequence-independent endonuclease. I don't know how can you implement this int he workflow... Best wishes, Lucia

…

________________________________ From: JIANHONG OU ***@***.***> Sent: Friday, April 26, 2024 6:50 PM To: nf-core/hicar ***@***.***> Cc: Lucia Zifcakova ***@***.***>; Author ***@***.***> Subject: Re: [nf-core/hicar] Java heap space (Issue #108) Could you please let me know the enzyme? I can add it. My apologies that I did not write full documentation for that.Best!Your sincerely,Jianhong OuOn Apr 26, 2024, at 5:05 AM, luciazifcakova ***@***.***> wrote: Dear Jianhong, thank you for the information, it helped. I actually have Omni-C data that were cut by DNAse I but it is not on the list of enzymes. Can I add my own enzyme to the pipeline somehow? Best wishes, Lucia

________________________________ From: JIANHONG OU ***@***.***> Sent: Monday, April 22, 2024 10:40 PM To: nf-core/hicar ***@***.***> Cc: Lucia Zifcakova ***@***.***>; Author ***@***.***> Subject: Re: [nf-core/hicar] Java heap space (Issue #108) Try to add macs_gsize to your parameter list to avoid loading huge genome into the memory. And there is a typo in your script at -profile oist, singularity. Should be -profile oist,singularity — Reply to this email directly, view it on GitHub<#108 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AWQLEWBNMHLFOGUYAX2P57LY6UHLTAVCNFSM6AAAAABF757ORSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANRZGQ3TMMBXG4>. You are receiving this because you authored the thread.Message ID: ***@***.***> —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you commented.Message ID: ***@***.***> — Reply to this email directly, view it on GitHub<#108 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AWQLEWE4WJNCOSIL3DSDMJDY7IPP3AVCNFSM6AAAAABF757ORSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANZZGAZTKOJVGU>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[jianhong]

Sorry for the delay. Maybe hicar pipeline is not the best pipeline for you to analysis Omni-C. I can adjust the pipeline by adding skip parameter to skip the parse selection based on cutting site in the same fragment and also skip the cutting sites counting for interaction calling. However, I am afraid this change will take time. Jianhong. From: luciazifcakova ***@***.***> Date: Monday, April 29, 2024 at 7:16 PM To: nf-core/hicar ***@***.***> Cc: JIANHONG OU ***@***.***>, Comment ***@***.***> Subject: Re: [nf-core/hicar] Java heap space (Issue #108) Dear Jianhong, Omni-C use this enzyme: DNase I, a sequence-independent endonuclease. I don't know how can you implement this int he workflow... Best wishes, Lucia

…

________________________________ From: JIANHONG OU ***@***.***> Sent: Friday, April 26, 2024 6:50 PM To: nf-core/hicar ***@***.***> Cc: Lucia Zifcakova ***@***.***>; Author ***@***.***> Subject: Re: [nf-core/hicar] Java heap space (Issue #108) Could you please let me know the enzyme? I can add it. My apologies that I did not write full documentation for that.Best!Your sincerely,Jianhong OuOn Apr 26, 2024, at 5:05 AM, luciazifcakova ***@***.***> wrote: Dear Jianhong, thank you for the information, it helped. I actually have Omni-C data that were cut by DNAse I but it is not on the list of enzymes. Can I add my own enzyme to the pipeline somehow? Best wishes, Lucia

________________________________ From: JIANHONG OU ***@***.***> Sent: Monday, April 22, 2024 10:40 PM To: nf-core/hicar ***@***.***> Cc: Lucia Zifcakova ***@***.***>; Author ***@***.***> Subject: Re: [nf-core/hicar] Java heap space (Issue #108) Try to add macs_gsize to your parameter list to avoid loading huge genome into the memory. And there is a typo in your script at -profile oist, singularity. Should be -profile oist,singularity — Reply to this email directly, view it on GitHub<#108 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AWQLEWBNMHLFOGUYAX2P57LY6UHLTAVCNFSM6AAAAABF757ORSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANRZGQ3TMMBXG4>. You are receiving this because you authored the thread.Message ID: ***@***.***> —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you commented.Message ID: ***@***.***> — Reply to this email directly, view it on GitHub<#108 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AWQLEWE4WJNCOSIL3DSDMJDY7IPP3AVCNFSM6AAAAABF757ORSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANZZGAZTKOJVGU>. You are receiving this because you authored the thread.Message ID: ***@***.***> — Reply to this email directly, view it on GitHub<#108 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABLBEA46GLSMBPB63MYFAEDY73IELAVCNFSM6AAAAABF757ORSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBTHA2DENJWHE>. You are receiving this because you commented.Message ID: ***@***.***>