Unexpected end of ZLIB input stream
syfobfx opened this issue · comments
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 streamjava.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.
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.