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Buffer underflow on -resume #121

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syfobfx opened this issue Mar 18, 2022 · 0 comments
Open

Buffer underflow on -resume #121

syfobfx opened this issue Mar 18, 2022 · 0 comments

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@syfobfx
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syfobfx commented Mar 18, 2022

Hi all,

I am getting a Buffer underflow error while running the pipeline with the -resume option, after a failed run.

The command line is:

nextflow run nf-core/hic
-revision 1.3.0
-profile genotoul
-resume
-c /work2/project/bovreg/results/hic/nfcoreruns/Run_pool_BOVREGH2020.18981.conf
-work-dir /work2/project/bovreg/results/hic/nfcoreruns/Run_pool_BOVREGH2020.18981/work
--fasta /work2/project/bovreg/data/genome/ARS-UCD1.2_Btau5.0.1Y.fa
--bwt2_index /work2/project/bovreg/data/genome
--outdir /work2/project/bovreg/results/hic/nfcoreruns/Run_pool_BOVREGH2020.18981
--input '/work2/project/bovreg/data/reads/hic/Run_pool_BOVREGH2020.18981/*R{1,2}.fastq.gz'
--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 --reorder'
--min_mapq 10
--digestion 'arima'
--chromosome_size /work2/project/bovreg/data/genome/ARS-UCD1.2_Btau5.0.1Y.fa.chromlen
--min_insert_size 20
--max_insert_size 1000
--bin_size '1000000,200000,50000,10000,1000'
--save_interaction_bam
--hicpro_maps
--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'
--split_fastq --fastq_chunks_size 10000000

The log file is attached
Run_pool_BOVREGH2020.18981.log

The previous log file is also attached.
Run_pool_BOVREGH2020.18981.bk.log

I tried to solve that original issue by just extending the time value of the trim_reads process in the config file and by running the same command again, but this is how I got that Buffer underflow error.

Thanks a lot for the assistance.

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