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Java heap space #108

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luciazifcakova opened this issue Apr 10, 2024 · 5 comments
Open

Java heap space #108

luciazifcakova opened this issue Apr 10, 2024 · 5 comments
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@luciazifcakova
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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
@luciazifcakova luciazifcakova added the bug Something isn't working label Apr 10, 2024
@jianhong
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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
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luciazifcakova commented Apr 26, 2024 via email

@jianhong
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jianhong commented Apr 26, 2024 via email

@luciazifcakova
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luciazifcakova commented Apr 29, 2024 via email

@jianhong
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jianhong commented May 9, 2024 via email

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@jianhong @luciazifcakova