/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/NfCoreEager_2026-03-24--15-47-18/scripts/Metagenomics_NextSeq500_20190507_NS278_o5638_subSampled_2185.sh_sushiID3619_2026-03-24--15-47-26_o.log -------------------------------------------------- Job runs on fgcz-c-095 at /scratch/NfCoreEager_2026-03-24--15-47-18_temp3418060 sample 1 S1_undiff 2 S2_undiff 3 S3_undiff 4 S4_diff 5 S5_diff 6 S6_diff fastq_1 1 /srv/GT/analysis/course_sushi/public/gstore/projects/p1000/NextSeq500_20190507_NS278_o5638_subSampled/20190507.A-S1a_undiff_R1-subsample.fastq.gz 2 /srv/GT/analysis/course_sushi/public/gstore/projects/p1000/NextSeq500_20190507_NS278_o5638_subSampled/20190507.A-S2_undiff_R1-subsample.fastq.gz 3 /srv/GT/analysis/course_sushi/public/gstore/projects/p1000/NextSeq500_20190507_NS278_o5638_subSampled/20190507.A-S3_undiff_R1-subsample.fastq.gz 4 /srv/GT/analysis/course_sushi/public/gstore/projects/p1000/NextSeq500_20190507_NS278_o5638_subSampled/20190507.A-S4_diff_R1-subsample.fastq.gz 5 /srv/GT/analysis/course_sushi/public/gstore/projects/p1000/NextSeq500_20190507_NS278_o5638_subSampled/20190507.A-S5_diff_R1-subsample.fastq.gz 6 /srv/GT/analysis/course_sushi/public/gstore/projects/p1000/NextSeq500_20190507_NS278_o5638_subSampled/20190507.A-S6_diff_R1-subsample.fastq.gz N E X T F L O W ~ version 25.10.4 Pulling nf-core/eager ... downloaded from https://github.com/nf-core/eager.git ___STDOUT_END___ /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/NfCoreEager_2026-03-24--15-47-18/scripts/Metagenomics_NextSeq500_20190507_NS278_o5638_subSampled_2185.sh_sushiID3619_2026-03-24--15-47-26_e.log -------------------------------------------------- + set -o pipefail + umask 0002 + SCRATCH_DIR=/scratch/NfCoreEager_2026-03-24--15-47-18_temp3418060 + GSTORE_DIR=/srv/GT/analysis/course_sushi/public/gstore/projects + INPUT_DATASET=/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/NfCoreEager_2026-03-24--15-47-18/input_dataset.tsv + LAST_JOB=TRUE ++ hostname + echo 'Job runs on fgcz-c-095' + echo 'at /scratch/NfCoreEager_2026-03-24--15-47-18_temp3418060' + mkdir /scratch/NfCoreEager_2026-03-24--15-47-18_temp3418060 + cd /scratch/NfCoreEager_2026-03-24--15-47-18_temp3418060 + source /usr/local/ngseq/etc/lmod_profile +++ eval 'echo /usr/local/ngseq/etc/modules:/etc/fgcz-envmods/lmod:/etc/lmod/modules:/usr/share/lmod/lmod/modulefiles' ++++ echo /usr/local/ngseq/etc/modules:/etc/fgcz-envmods/lmod:/etc/lmod/modules:/usr/share/lmod/lmod/modulefiles ++ export MODULEPATH=/usr/local/ngseq/etc/modules:/usr/local/ngseq/etc/modules:/etc/fgcz-envmods/lmod:/etc/lmod/modules:/usr/share/lmod/lmod/modulefiles ++ MODULEPATH=/usr/local/ngseq/etc/modules:/usr/local/ngseq/etc/modules:/etc/fgcz-envmods/lmod:/etc/lmod/modules:/usr/share/lmod/lmod/modulefiles ++ source /usr/share/lmod/lmod/init/profile +++ '[' -z '' ']' +++ LMOD_ALLOW_ROOT_USE=yes +++ '[' -n '' ']' +++ '[' yes '!=' yes ']' +++ '[' -z /usr/share/modulefiles ']' +++ findExec READLINK_CMD /bin/readlink readlink +++ Nm=READLINK_CMD +++ confPath=/bin/readlink +++ execNm=readlink +++ eval READLINK_CMD=/bin/readlink ++++ READLINK_CMD=/bin/readlink +++ '[' '!' -x /bin/readlink ']' +++ unset Nm confPath execNm +++ findExec PS_CMD /bin/ps ps +++ Nm=PS_CMD +++ confPath=/bin/ps +++ execNm=ps +++ eval PS_CMD=/bin/ps ++++ PS_CMD=/bin/ps +++ '[' '!' -x /bin/ps ']' +++ unset Nm confPath execNm +++ findExec EXPR_CMD /usr/bin/expr expr +++ Nm=EXPR_CMD +++ confPath=/usr/bin/expr +++ execNm=expr +++ eval EXPR_CMD=/usr/bin/expr ++++ EXPR_CMD=/usr/bin/expr +++ '[' '!' -x /usr/bin/expr ']' +++ unset Nm confPath execNm +++ findExec BASENAME_CMD /usr/bin/basename basename +++ Nm=BASENAME_CMD +++ confPath=/usr/bin/basename +++ execNm=basename +++ eval BASENAME_CMD=/usr/bin/basename ++++ BASENAME_CMD=/usr/bin/basename +++ '[' '!' -x /usr/bin/basename ']' +++ unset Nm confPath execNm +++ unset -f findExec +++ '[' -f /proc/3418060/exe ']' ++++ /bin/readlink /proc/3418060/exe +++ my_shell=/usr/bin/bash ++++ /usr/bin/expr /usr/bin/bash : '-*\(.*\)' +++ my_shell=/usr/bin/bash ++++ /usr/bin/basename /usr/bin/bash +++ my_shell=bash +++ case ${my_shell} in +++ '[' -f /usr/share/lmod/lmod/init/bash ']' +++ . /usr/share/lmod/lmod/init/bash ++++ '[' -z '' ']' ++++ case "$-" in ++++ __lmod_vx=x ++++ '[' -n x ']' ++++ set +x Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for this output (/usr/share/lmod/lmod/init/bash) Shell debugging restarted ++++ unset __lmod_vx +++ unset my_shell PS_CMD EXPR_CMD BASENAME_CMD MODULEPATH_INIT LMOD_ALLOW_ROOT_USE READLINK_CMD ++ export NGSEQ=/usr/local/ngseq ++ NGSEQ=/usr/local/ngseq ++ export ngsrc=/usr/local/ngseq/srcm ++ ngsrc=/usr/local/ngseq/srcm ++ export ngpkg=/usr/local/ngseq/packages ++ ngpkg=/usr/local/ngseq/packages ++ export ngmdf=/usr/local/ngseq/etc/modules ++ ngmdf=/usr/local/ngseq/etc/modules ++ '[' -d /usr/local/ngseq/. ']' ++ PATH=/usr/local/ngseq/bin:/home/trxcopy/.conda/envs/gi_sushi_jobmanager_2024/bin:/misc/ngseq12/miniforge3/condabin:/usr/local/ngseq/packages/Dev/Ruby/3.3.7/bin:/usr/local/ngseq/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games ++ export PATH ++ LD_LIBRARY_PATH=/usr/local/ngseq/lib:/usr/local/ngseq/lib:/usr/local/ngseq/lib ++ export LD_LIBRARY_PATH ++ alias 'lmodInit=. /usr/local/ngseq/etc/lmod_profile' + export NXF_SINGULARITY_CACHEDIR=/misc/fgcz01/nextflow_apptainer_cache/ + NXF_SINGULARITY_CACHEDIR=/misc/fgcz01/nextflow_apptainer_cache/ + export SINGULARITY_CACHEDIR=/misc/fgcz01/nextflow_apptainer_cache/ + SINGULARITY_CACHEDIR=/misc/fgcz01/nextflow_apptainer_cache/ + R --vanilla --slave Loading required package: data.table Loading required package: Biostrings Loading required package: BiocGenerics Loading required package: generics Attaching package: ‘generics’ The following objects are masked from ‘package:base’: as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:data.table’: first, second The following object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:base’: expand.grid, I, unname Loading required package: IRanges Attaching package: ‘IRanges’ The following object is masked from ‘package:data.table’: shift Loading required package: XVector Loading required package: GenomeInfoDb Attaching package: ‘Biostrings’ The following object is masked from ‘package:base’: strsplit Loading required package: GenomicRanges Loading required package: tidyverse ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ── ✔ dplyr 1.1.4 ✔ readr 2.1.5 ✔ forcats 1.0.1 ✔ stringr 1.6.0 ✔ ggplot2 4.0.1 ✔ tibble 3.3.1 ✔ lubridate 1.9.4 ✔ tidyr 1.3.2 ✔ purrr 1.1.0 ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ── ✖ lubridate::%within%() masks IRanges::%within%() ✖ dplyr::between() masks data.table::between() ✖ dplyr::collapse() masks Biostrings::collapse(), IRanges::collapse() ✖ dplyr::combine() masks BiocGenerics::combine() ✖ purrr::compact() masks XVector::compact() ✖ dplyr::desc() masks IRanges::desc() ✖ tidyr::expand() masks S4Vectors::expand() ✖ dplyr::filter() masks stats::filter() ✖ dplyr::first() masks S4Vectors::first(), data.table::first() ✖ lubridate::hour() masks data.table::hour() ✖ lubridate::isoweek() masks data.table::isoweek() ✖ lubridate::isoyear() masks data.table::isoyear() ✖ dplyr::lag() masks stats::lag() ✖ dplyr::last() masks data.table::last() ✖ lubridate::mday() masks data.table::mday() ✖ lubridate::minute() masks data.table::minute() ✖ lubridate::month() masks data.table::month() ✖ ggplot2::Position() masks BiocGenerics::Position(), base::Position() ✖ lubridate::quarter() masks data.table::quarter() ✖ purrr::reduce() masks GenomicRanges::reduce(), IRanges::reduce() ✖ dplyr::rename() masks S4Vectors::rename() ✖ lubridate::second() masks S4Vectors::second(), data.table::second() ✖ lubridate::second<-() masks S4Vectors::second<-() ✖ dplyr::slice() masks XVector::slice(), IRanges::slice() ✖ purrr::transpose() masks data.table::transpose() ✖ lubridate::wday() masks data.table::wday() ✖ lubridate::week() masks data.table::week() ✖ lubridate::yday() masks data.table::yday() ✖ lubridate::year() masks data.table::year() ℹ Use the conflicted package () to force all conflicts to become errors Loading required package: logger Sample sheet written to: samplesheet.csv Sample sheet contents: Custom config written: custom_resources.config // Executor: total available resources for this job executor { name = 'local' cpus = 16 memory = '128.GB' } // Cap all process labels to fit within executor limits process { resourceLimits = [ cpus: 16, memory: '128.GB' ] } Loading module: nextflow/25.10 Loading Nextflow 25.10.4 Using FASTA: /srv/GT/reference/Mus_musculus/GENCODE/GRCm39/Sequence/WholeGenomeFasta/genome.fa Using GTF: /srv/GT/reference/Mus_musculus/GENCODE/GRCm39/Annotation/Release_M37-2025-07-03/Genes/genes.gtf Running command: nextflow run nf-core/eager -r 2.5.3 --input samplesheet.csv --outdir _result -profile singularity -c custom_resources.config --fasta /srv/GT/reference/Mus_musculus/GENCODE/GRCm39/Sequence/WholeGenomeFasta/genome.fa --gtf /srv/GT/reference/Mus_musculus/GENCODE/GRCm39/Annotation/Release_M37-2025-07-03/Genes/genes.gtf --udg_type 'none' --single_stranded 'false' --single_end 'false' --colour_chemistry '4' --bam 'false' --run_convertinputbam 'false' --large_ref 'false' --save_reference 'false' --skip_fastqc 'false' --skip_adapterremoval 'false' --skip_preseq 'false' --skip_deduplication 'false' --skip_damage_calculation 'false' --skip_qualimap 'false' --complexity_filter_poly_g 'false' --complexity_filter_poly_g_min '10' --clip_forward_adaptor 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' --clip_reverse_adaptor 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA' --clip_readlength '30' --clip_min_read_quality '20' --min_adap_overlap '1' --skip_collapse 'false' --skip_trim 'false' --preserve5p 'false' --mergedonly 'false' --qualitymax '41' --run_post_ar_trimming 'false' --post_ar_trim_front '7' --post_ar_trim_tail '7' --post_ar_trim_front2 '7' --post_ar_trim_tail2 '7' --mapper 'bwaaln' --bwaalnn '0.01' --bwaalnk '2' --bwaalnl '1024' --bwaalno '2' --circularextension '500' --circulartarget 'MT' --circularfilter 'false' --bt2_alignmode 'local' --bt2_sensitivity 'no-preset' --bt2n '0' --bt2l '0' --bt2_trim5 '0' --bt2_trim3 '0' --bt2_maxins '500' --hostremoval_input_fastq 'false' --hostremoval_mode 'strip' --run_bam_filtering 'false' --bam_mapping_quality_threshold '0' --bam_filter_minreadlength '0' --bam_unmapped_type 'discard' --dedupper 'markduplicates' --dedup_all_merged 'false' --preseq_mode 'c_curve' --preseq_step_size '1000' --preseq_maxextrap '10000000000' --preseq_terms '100' --preseq_bootstrap '100' --preseq_cval '0.95' --damage_calculation_tool 'damageprofiler' --damageprofiler_length '100' --damageprofiler_threshold '15' --damageprofiler_yaxis '0.3' --mapdamage_downsample '0' --mapdamage_yaxis '0.3' --run_pmdtools 'false' --pmdtools_range '10' --pmdtools_threshold '3' --pmdtools_max_reads '10000' --pmdtools_platypus 'false' --run_mapdamage_rescaling 'false' --rescale_seqlength '12' --rescale_length_5p '0' --rescale_length_3p '0' --run_bedtools_coverage 'false' --anno_file_is_unsorted 'false' --run_trim_bam 'false' --bamutils_clip_double_stranded_half_udg_left '0' --bamutils_clip_double_stranded_half_udg_right '0' --bamutils_clip_double_stranded_none_udg_left '0' --bamutils_clip_double_stranded_none_udg_right '0' --bamutils_clip_single_stranded_half_udg_left '0' --bamutils_clip_single_stranded_half_udg_right '0' --bamutils_clip_single_stranded_none_udg_left '0' --bamutils_clip_single_stranded_none_udg_right '0' --bamutils_softclip 'false' --run_genotyping 'false' --genotyping_tool 'ug' --genotyping_source 'raw' --gatk_call_conf '30' --gatk_ploidy '2' --gatk_downsample '250' --gatk_hc_out_mode 'EMIT_ALL_ACTIVE_SITES' --gatk_hc_emitrefconf 'NONE' --gatk_ug_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --gatk_ug_keep_realign_bam 'false' --freebayes_C '1' --freebayes_g '0' --freebayes_p '2' --pileupcaller_method 'randomHaploid' --pileupcaller_transitions_mode 'AllSites' --pileupcaller_min_map_quality '30' --pileupcaller_min_base_quality '30' --angsd_glmodel 'samtools' --angsd_glformat 'text' --angsd_createfasta 'false' --angsd_fastamethod 'random' --run_bcftools_stats 'true' --run_vcf2genome 'false' --vcf2genome_minc '5' --vcf2genome_minq '30' --vcf2genome_minfreq '0.8' --run_multivcfanalyzer 'false' --write_allele_frequencies 'false' --min_genotype_quality '30' --min_base_coverage '5' --min_allele_freq_hom '0.9' --min_allele_freq_het '0.9' --reference_gff_annotations 'NA' --reference_gff_exclude 'NA' --snp_eff_results 'NA' --run_mtnucratio 'false' --mtnucratio_header 'MT' --run_sexdeterrmine 'false' --run_nuclear_contamination 'false' --contamination_chrom_name 'X' --metagenomic_complexity_filter 'false' --metagenomic_complexity_entropy '0.3' --run_metagenomic_screening 'false' --metagenomic_min_support_reads '1' --percent_identity '85' --malt_mode 'BlastN' --malt_alignment_mode 'Local' --malt_top_percent '1' --malt_min_support_mode 'percent' --malt_min_support_percent '0.01' --malt_max_queries '100' --malt_memory_mode 'load' --malt_sam_output 'false' --run_maltextract 'false' --maltextract_filter 'def_anc' --maltextract_toppercent '0.01' --maltextract_destackingoff 'false' --maltextract_downsamplingoff 'false' --maltextract_duplicateremovaloff 'false' --maltextract_matches 'false' --maltextract_megansummary 'false' --maltextract_percentidentity '85' --maltextract_topalignment 'false' INFO (ezRun) [2026-03-24 15:47:41] EXECUTED CMD: nextflow run nf-core/eager -r 2.5.3 --input samplesheet.csv --outdir _result -profile singularity -c custom_resources.config --fasta /srv/GT/reference/Mus_musculus/GENCODE/GRCm39/Sequence/WholeGenomeFasta/genome.fa --gtf /srv/GT/reference/Mus_musculus/GENCODE/GRCm39/Annotation/Release_M37-2025-07-03/Genes/genes.gtf --udg_type 'none' --single_stranded 'false' --single_end 'false' --colour_chemistry '4' --bam 'false' --run_convertinputbam 'false' --large_ref 'false' --save_reference 'false' --skip_fastqc 'false' --skip_adapterremoval 'false' --skip_preseq 'false' --skip_deduplication 'false' --skip_damage_calculation 'false' --skip_qualimap 'false' --complexity_filter_poly_g 'false' --complexity_filter_poly_g_min '10' --clip_forward_adaptor 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' --clip_reverse_adaptor 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA' --clip_readlength '30' --clip_min_read_quality '20' --min_adap_overlap '1' --skip_collapse 'false' --skip_trim 'false' --preserve5p 'false' --mergedonly 'false' --qualitymax '41' --run_post_ar_trimming 'false' --post_ar_trim_front '7' --post_ar_trim_tail '7' --post_ar_trim_front2 '7' --post_ar_trim_tail2 '7' --mapper 'bwaaln' --bwaalnn '0.01' --bwaalnk '2' --bwaalnl '1024' --bwaalno '2' --circularextension '500' --circulartarget 'MT' --circularfilter 'false' --bt2_alignmode 'local' --bt2_sensitivity 'no-preset' --bt2n '0' --bt2l '0' --bt2_trim5 '0' --bt2_trim3 '0' --bt2_maxins '500' --hostremoval_input_fastq 'false' --hostremoval_mode 'strip' --run_bam_filtering 'false' --bam_mapping_quality_threshold '0' --bam_filter_minreadlength '0' --bam_unmapped_type 'discard' --dedupper 'markduplicates' --dedup_all_merged 'false' --preseq_mode 'c_curve' --preseq_step_size '1000' --preseq_maxextrap '10000000000' --preseq_terms '100' --preseq_bootstrap '100' --preseq_cval '0.95' --damage_calculation_tool 'damageprofiler' --damageprofiler_length '100' --damageprofiler_threshold '15' --damageprofiler_yaxis '0.3' --mapdamage_downsample '0' --mapdamage_yaxis '0.3' --run_pmdtools 'false' --pmdtools_range '10' --pmdtools_threshold '3' --pmdtools_max_reads '10000' --pmdtools_platypus 'false' --run_mapdamage_rescaling 'false' --rescale_seqlength '12' --rescale_length_5p '0' --rescale_length_3p '0' --run_bedtools_coverage 'false' --anno_file_is_unsorted 'false' --run_trim_bam 'false' --bamutils_clip_double_stranded_half_udg_left '0' --bamutils_clip_double_stranded_half_udg_right '0' --bamutils_clip_double_stranded_none_udg_left '0' --bamutils_clip_double_stranded_none_udg_right '0' --bamutils_clip_single_stranded_half_udg_left '0' --bamutils_clip_single_stranded_half_udg_right '0' --bamutils_clip_single_stranded_none_udg_left '0' --bamutils_clip_single_stranded_none_udg_right '0' --bamutils_softclip 'false' --run_genotyping 'false' --genotyping_tool 'ug' --genotyping_source 'raw' --gatk_call_conf '30' --gatk_ploidy '2' --gatk_downsample '250' --gatk_hc_out_mode 'EMIT_ALL_ACTIVE_SITES' --gatk_hc_emitrefconf 'NONE' --gatk_ug_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --gatk_ug_keep_realign_bam 'false' --freebayes_C '1' --freebayes_g '0' --freebayes_p '2' --pileupcaller_method 'randomHaploid' --pileupcaller_transitions_mode 'AllSites' --pileupcaller_min_map_quality '30' --pileupcaller_min_base_quality '30' --angsd_glmodel 'samtools' --angsd_glformat 'text' --angsd_createfasta 'false' --angsd_fastamethod 'random' --run_bcftools_stats 'true' --run_vcf2genome 'false' --vcf2genome_minc '5' --vcf2genome_minq '30' --vcf2genome_minfreq '0.8' --run_multivcfanalyzer 'false' --write_allele_frequencies 'false' --min_genotype_quality '30' --min_base_coverage '5' --min_allele_freq_hom '0.9' --min_allele_freq_het '0.9' --reference_gff_annotations 'NA' --reference_gff_exclude 'NA' --snp_eff_results 'NA' --run_mtnucratio 'false' --mtnucratio_header 'MT' --run_sexdeterrmine 'false' --run_nuclear_contamination 'false' --contamination_chrom_name 'X' --metagenomic_complexity_filter 'false' --metagenomic_complexity_entropy '0.3' --run_metagenomic_screening 'false' --metagenomic_min_support_reads '1' --percent_identity '85' --malt_mode 'BlastN' --malt_alignment_mode 'Local' --malt_top_percent '1' --malt_min_support_mode 'percent' --malt_min_support_percent '0.01' --malt_max_queries '100' --malt_memory_mode 'load' --malt_sam_output 'false' --run_maltextract 'false' --maltextract_filter 'def_anc' --maltextract_toppercent '0.01' --maltextract_destackingoff 'false' --maltextract_downsamplingoff 'false' --maltextract_duplicateremovaloff 'false' --maltextract_matches 'false' --maltextract_megansummary 'false' --maltextract_percentidentity '85' --maltextract_topalignment 'false' Nextflow DSL1 is no longer supported — Update your script to DSL2, or use Nextflow 22.10.x or earlier Error in ezSystem(cmd) : nextflow run nf-core/eager -r 2.5.3 --input samplesheet.csv --outdir _result -profile singularity -c custom_resources.config --fasta /srv/GT/reference/Mus_musculus/GENCODE/GRCm39/Sequence/WholeGenomeFasta/genome.fa --gtf /srv/GT/reference/Mus_musculus/GENCODE/GRCm39/Annotation/Release_M37-2025-07-03/Genes/genes.gtf --udg_type 'none' --single_stranded 'false' --single_end 'false' --colour_chemistry '4' --bam 'false' --run_convertinputbam 'false' --large_ref 'false' --save_reference 'false' --skip_fastqc 'false' --skip_adapterremoval 'false' --skip_preseq 'false' --skip_deduplication 'false' --skip_damage_calculation 'false' --skip_qualimap 'false' --complexity_filter_poly_g 'false' --complexity_filter_poly_g_min '10' --clip_forward_adaptor 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' --clip_reverse_adaptor 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA' --clip_readlength '30' --clip_min_read_quality '20' --min_adap_overlap '1' --skip_collapse 'false' --skip_trim 'false' --preserve5p 'false' --mer Calls: -> ezSystem Execution halted ___STDERR_END___