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nf-core / hic

Analysis of Chromosome Conformation Capture data (Hi-C)
https://nf-co.re/hic
MIT License
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Unexpected end of ZLIB input stream #137

Closed syfobfx closed 1 year ago

syfobfx commented 2 years ago

Description of the bug

The pipeline ends during the bowtie process with this error message at the end of the log:

Unexpected end of ZLIB input stream

java.nio.channels.ClosedByInterruptException

-[nf-core/hic] Pipeline completed with errors-

Launching script

cat capturehic2.sh

#!/bin/bash
#SBATCH -J capturehic2
#SBATCH -e /work/project/fragencode/workspace/geneswitch/results/hic/sus_scrofa/capturehic2.err
#SBATCH -o /work/project/fragencode/workspace/geneswitch/results/hic/sus_scrofa/capturehic2.log
#SBATCH -p unlimitq
#SBATCH --mail-type=END,FAIL
#SBATCH --export=ALL 
#SBATCH --cpus-per-task=1
#SBATCH --mem=4G

mkdir -p /work/project/fragencode/workspace/geneswitch/results/hic/sus_scrofa/capturehic2
cd /work/project/fragencode/workspace/geneswitch/results/hic/sus_scrofa/capturehic2
module load bioinfo/nfcore-Nextflow-v21.10.6

nextflow run nf-core/hic \
 -revision    1.3.0 \
 -profile     genotoul \
 -resume              \
 -c           /work/project/fragencode/workspace/geneswitch/results/hic/sus_scrofa/capturehic2.conf \
 -work-dir    /work/project/fragencode/workspace/geneswitch/results/hic/sus_scrofa/capturehic2/work \
 --fasta      /work/project/fragencode/data/species/sus_scrofa/Sscrofa11.1/sus_scrofa.fa \
 --bwt2_index /work/project/fragencode/data/species/sus_scrofa/Sscrofa11.1 \
 --outdir     /work/project/fragencode/workspace/geneswitch/results/hic/sus_scrofa/capturehic2 \
 --input      '/work/project/fragencode/workspace/geneswitch/data/hic/sus_scrofa/CHiC-[0-9]-*_R{1,2}.fastq.gz'\
 --bwt2_opts_end2end '-5 5 -3 95 --very-sensitive -L 20 --score-min L,-0.6,-0.3 --end-to-end --reorder' \
 --bwt2_opts_trimmed '--very-sensitive -L 20 --score-min L,-0.6,-0.3 --end-to-end --reorder' \
 --min_mapq 10 \
 --restriction_site '^GATC,G^ANTC' \
 --ligation_site 'GATCGATC,GANTGATC,GANTANTC,GATCANTC' \
 --chromosome_size /work/project/fragencode/data/species/sus_scrofa/Sscrofa11.1/chrom.len \
 --min_insert_size 10 \
 --max_insert_size 1000 \
 --bin_size                  '500000,10000,5000,1000' \
 --ice_max_iter     100 \
 --ice_filter_low_count_perc  0.02 \
 --ice_filter_high_count_perc 0 \
 --ice_eps     0.1 \
 --res_compartments          '500000,200000' \
 --tads_caller               'insulation,hicexplorer' \
 --res_tads                  '100000,50000' \
 --save_interaction_bam \
 --skip_balancing \
 --split_fastq --fastq_chunks_size 20000000

Log files

End of the output:

executor > slurm (27) [41/d990b9] process > get_software_versions [100%] 1 of 1 ✔ [87/46f6de] process > getRestrictionFragments (su... [100%] 1 of 1 ✔ [86/780ee7] process > bowtie2_end_to_end (CHiC_R1.6) [100%] 6 of 6 [54/ee1541] process > trim_reads (CHiC_R1.6) [100%] 6 of 6 [66/c98141] process > bowtie2_on_trimmed_reads (C... [100%] 6 of 6 [32/735751] process > bowtie2_merge_mapping_steps... [100%] 6 of 6 [- ] process > combine_mates - [- ] process > get_valid_interaction - [- ] process > remove_duplicates - [- ] process > merge_stats - [- ] process > build_contact_maps - [- ] process > run_ice - [- ] process > convert_to_pairs - [- ] process > cooler_raw - [- ] process > cooler_balance - [- ] process > cooler_zoomify - [- ] process > dist_decay - [- ] process > compartment_calling - [- ] process > tads_hicexplorer - [- ] process > tads_insulation - [- ] process > multiqc - [f0/2ecfd3] process > output_documentation [100%] 1 of 1 ✔

  • Ignore this warning: params.schema_ignore_params = "igenomesIgnore" WARN: Found unexpected parameters:
  • --igenomesIgnore: true Unexpected end of ZLIB input stream

java.nio.channels.ClosedByInterruptException

-[nf-core/hic] Pipeline completed with errors-

complete log file here

Additional context

Probably an issue about the input files but a more explicit error message would be nice.

syfobfx commented 2 years ago

As suspected, the explanation was an issue with the input fastq files. The error message could indicate the issue more clearly and maybe precise the problematic file. Thanks.