/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/o35755_AtacENCODE_2025-07-24--16-43-39/scripts/QC_mut11_ventricles_100k_1.sh_sushiID1621_2025-07-24--16-43-50_o.log -------------------------------------------------- Job runs on fgcz-c-095 at /scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut11_temp2429899 Starting EzAppAtacENCODE AtacENCODE o35755_AtacENCODE_2025-07-24--16-43-39_mut11_temp2429899 2025-07-24 16:43:58 ezRun tag: ab8b8bb744696ce1f0c18d74d7827aa49a033ee7 ezRun github link: https://github.com/uzh/ezRun/tree/ab8b8bb744696ce1f0c18d74d7827aa49a033ee7 R version 4.5.0 (2025-04-11) Platform: x86_64-pc-linux-gnu Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0 LAPACK version 3.11.0 locale: [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C time zone: Europe/Berlin tzcode source: system (glibc) attached base packages: [1] stats4 stats graphics grDevices utils datasets methods [8] base other attached packages: [1] rjson_0.2.23 ezRun_3.21.1 lubridate_1.9.4 [4] forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 [7] purrr_1.0.4 readr_2.1.5 tidyr_1.3.1 [10] tibble_3.2.1 ggplot2_3.5.2 tidyverse_2.0.0 [13] GenomicRanges_1.60.0 Biostrings_2.76.0 GenomeInfoDb_1.44.0 [16] XVector_0.48.0 IRanges_2.42.0 S4Vectors_0.46.0 [19] BiocGenerics_0.54.0 generics_0.1.4 data.table_1.17.4 loaded via a namespace (and not attached): [1] gtable_0.3.6 jsonlite_2.0.0 compiler_4.5.0 [4] crayon_1.5.3 tidyselect_1.2.1 dichromat_2.0-0.1 [7] scales_1.4.0 R6_2.6.1 GenomeInfoDbData_1.2.14 [10] pillar_1.10.2 RColorBrewer_1.1-3 tzdb_0.5.0 [13] rlang_1.1.6 stringi_1.8.7 timechange_0.3.0 [16] cli_3.6.5 withr_3.0.2 magrittr_2.0.3 [19] grid_4.5.0 hms_1.1.3 lifecycle_1.0.4 [22] vctrs_0.6.5 glue_1.8.0 farver_2.1.2 [25] httr_1.4.7 tools_4.5.0 pkgconfig_2.0.3 [28] UCSC.utils_1.4.0 Finished EzAppAtacENCODE AtacENCODE o35755_AtacENCODE_2025-07-24--16-43-39_mut11_temp2429899 2025-07-24 17:03:09 [1] "Success" ___STDOUT_END___ /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/o35755_AtacENCODE_2025-07-24--16-43-39/scripts/QC_mut11_ventricles_100k_1.sh_sushiID1621_2025-07-24--16-43-50_e.log -------------------------------------------------- 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 1.0.0 ✔ stringr 1.5.1 ✔ ggplot2 3.5.2 ✔ tibble 3.2.1 ✔ lubridate 1.9.4 ✔ tidyr 1.3.1 ✔ purrr 1.0.4 ── 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() ✖ 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 unknown param: partition unknown param: sushi_app unknown param: isLastJob Loading required package: rjson 2025-07-24 16:44:09,923|caper.cli|INFO| Cromwell stdout: /scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut11_temp2429899/cromwell.out 2025-07-24 16:44:09,925|caper.caper_base|INFO| Creating a timestamped temporary directory. /scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut11_temp2429899/.caper_tmp/atac/20250724_164409_925369 2025-07-24 16:44:09,925|caper.caper_runner|INFO| Localizing files on work_dir. /scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut11_temp2429899/.caper_tmp/atac/20250724_164409_925369 2025-07-24 16:44:10,125|autouri.autouri|INFO| cp: (74e1c7f4) started. src=https://www.encodeproject.org/files/mm10_no_alt_analysis_set_ENCODE/@@download/mm10_no_alt_analysis_set_ENCODE.fasta.gz, dest=/scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut11_temp2429899/.caper_tmp/72041e824adb499a4974d85ba31fe30d/mm10_no_alt_analysis_set_ENCODE.fasta.gz 2025-07-24 16:45:00,824|autouri.autouri|INFO| cp: (74e1c7f4) done. 2025-07-24 16:45:00,826|autouri.autouri|INFO| cp: (38c49789) started. src=https://www.encodeproject.org/files/mm10_no_alt_analysis_set_ENCODE_mito_only/@@download/mm10_no_alt_analysis_set_ENCODE_mito_only.fasta.gz, dest=/scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut11_temp2429899/.caper_tmp/bbf176bc384fbe2a734ff0122b8315b3/mm10_no_alt_analysis_set_ENCODE_mito_only.fasta.gz 2025-07-24 16:45:02,122|autouri.autouri|INFO| cp: (38c49789) done. 2025-07-24 16:45:02,123|autouri.autouri|INFO| cp: (1eecbc53) started. src=https://www.encodeproject.org/files/ENCFF547MET/@@download/ENCFF547MET.bed.gz, dest=/scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut11_temp2429899/.caper_tmp/da42a1c4b0f9d3225600da56b2c9571d/ENCFF547MET.bed.gz 2025-07-24 16:45:03,475|autouri.autouri|INFO| cp: (1eecbc53) done. 2025-07-24 16:45:04,788|autouri.autouri|INFO| cp: (6e41c523) started. src=https://www.encodeproject.org/files/mm10_no_alt.chrom.sizes/@@download/mm10_no_alt.chrom.sizes.tsv, dest=/scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut11_temp2429899/.caper_tmp/a4733a4e097a19c869b1cb1aae1b33c9/mm10_no_alt.chrom.sizes.tsv 2025-07-24 16:45:06,037|autouri.autouri|INFO| cp: (6e41c523) done. 2025-07-24 16:45:06,037|autouri.autouri|INFO| cp: (e47bbdfc) started. src=https://www.encodeproject.org/files/ENCFF309GLL/@@download/ENCFF309GLL.tar.gz, dest=/scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut11_temp2429899/.caper_tmp/042925a7d9816ca478718df2aee1b980/ENCFF309GLL.tar.gz 2025-07-24 16:49:18,868|autouri.autouri|INFO| cp: (e47bbdfc) done. 2025-07-24 16:49:18,870|autouri.autouri|INFO| cp: (9cb6c471) started. src=https://www.encodeproject.org/files/mm10_no_alt_analysis_set_ENCODE_mito_only_bowtie2_index/@@download/mm10_no_alt_analysis_set_ENCODE_mito_only_bowtie2_index.tar.gz, dest=/scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut11_temp2429899/.caper_tmp/820a6f4379a41332ddf3f25fc09101d5/mm10_no_alt_analysis_set_ENCODE_mito_only_bowtie2_index.tar.gz 2025-07-24 16:49:20,533|autouri.autouri|INFO| cp: (9cb6c471) done. 2025-07-24 16:49:20,534|autouri.autouri|INFO| cp: (b10192a6) started. src=https://www.encodeproject.org/files/ENCFF018NEO/@@download/ENCFF018NEO.tar.gz, dest=/scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut11_temp2429899/.caper_tmp/506b880ea82aeae31802ecd4b265cff9/ENCFF018NEO.tar.gz 2025-07-24 16:53:16,146|autouri.autouri|INFO| cp: (b10192a6) done. 2025-07-24 16:53:16,148|autouri.autouri|INFO| cp: (9b15faef) started. src=https://www.encodeproject.org/files/mm10_no_alt_analysis_set_ENCODE_mito_only_bwa_index/@@download/mm10_no_alt_analysis_set_ENCODE_mito_only_bwa_index.tar.gz, dest=/scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut11_temp2429899/.caper_tmp/4ce6df75b5bc0d2c95fb08049d00b722/mm10_no_alt_analysis_set_ENCODE_mito_only_bwa_index.tar.gz 2025-07-24 16:53:17,493|autouri.autouri|INFO| cp: (9b15faef) done. 2025-07-24 16:53:17,493|autouri.autouri|INFO| cp: (fbf41dee) started. src=https://www.encodeproject.org/files/ENCFF454VOL/@@download/ENCFF454VOL.bed.gz, dest=/scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut11_temp2429899/.caper_tmp/4d2e30a0649d95b154163e7017f0b76c/ENCFF454VOL.bed.gz 2025-07-24 16:53:19,368|autouri.autouri|INFO| cp: (fbf41dee) done. 2025-07-24 16:53:19,369|autouri.autouri|INFO| cp: (cd534d6a) started. src=https://www.encodeproject.org/files/ENCFF015KVI/@@download/ENCFF015KVI.bed.gz, dest=/scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut11_temp2429899/.caper_tmp/b7f1373597857ea4d8a11c3915c4455d/ENCFF015KVI.bed.gz 2025-07-24 16:53:23,293|autouri.autouri|INFO| cp: (cd534d6a) done. 2025-07-24 16:53:23,293|autouri.autouri|INFO| cp: (04ba9fe4) started. src=https://www.encodeproject.org/files/ENCFF206BQS/@@download/ENCFF206BQS.bed.gz, dest=/scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut11_temp2429899/.caper_tmp/571f676aa2f98f5bffdb06c91453cffd/ENCFF206BQS.bed.gz 2025-07-24 16:53:24,958|autouri.autouri|INFO| cp: (04ba9fe4) done. 2025-07-24 16:53:24,959|autouri.autouri|INFO| cp: (9a30c597) started. src=https://www.encodeproject.org/files/ENCFF580RGZ/@@download/ENCFF580RGZ.bed.gz, dest=/scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut11_temp2429899/.caper_tmp/799bb08d7265d45d0a81bd65d6b7c7f0/ENCFF580RGZ.bed.gz 2025-07-24 16:53:28,671|autouri.autouri|INFO| cp: (9a30c597) done. 2025-07-24 16:53:28,672|autouri.autouri|INFO| cp: (13b6e60c) started. src=https://storage.googleapis.com/encode-pipeline-genome-data/mm10/ataqc/mm10_dnase_avg_fseq_signal_formatted.txt.gz, dest=/scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut11_temp2429899/.caper_tmp/cf2b604559fb2950d79aa439cafa86d0/mm10_dnase_avg_fseq_signal_formatted.txt.gz 2025-07-24 16:53:29,913|autouri.autouri|INFO| cp: (13b6e60c) done. 2025-07-24 16:53:29,914|autouri.autouri|INFO| cp: (4443a7c4) started. src=https://storage.googleapis.com/encode-pipeline-genome-data/mm10/ataqc/mm10_celltype_compare_subsample.bed.gz, dest=/scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut11_temp2429899/.caper_tmp/6cb5db6af37a5741fb86a6a9bf21f3f1/mm10_celltype_compare_subsample.bed.gz 2025-07-24 16:53:30,796|autouri.autouri|INFO| cp: (4443a7c4) done. 2025-07-24 16:53:30,796|autouri.autouri|INFO| cp: (a88b8a2c) started. src=https://storage.googleapis.com/encode-pipeline-genome-data/mm10/ataqc/mm10_dnase_avg_fseq_signal_metadata.txt, dest=/scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut11_temp2429899/.caper_tmp/fe37c3c5d22dfa5e5b26520a3ba8ac8f/mm10_dnase_avg_fseq_signal_metadata.txt 2025-07-24 16:53:30,953|autouri.autouri|INFO| cp: (a88b8a2c) done. 2025-07-24 16:53:31,633|caper.caper_workflow_opts|INFO| Singularity image found in WDL metadata. wdl=/usr/local/ngseq/src/atac-seq-pipeline/atac.wdl, s=https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/atac-seq-pipeline_v2.2.3.sif 2025-07-24 16:53:31,645|caper.cromwell|INFO| Installing Womtool JAR... https://github.com/broadinstitute/cromwell/releases/download/82/womtool-82.jar 2025-07-24 16:53:31,645|autouri.autouri|INFO| cp: (93427ff0) started. src=https://github.com/broadinstitute/cromwell/releases/download/82/womtool-82.jar, dest=/home/trxcopy/.caper/womtool_jar/womtool-82.jar 2025-07-24 16:53:32,295|autouri.autouri|INFO| cp: (93427ff0) skipped due to name_size_match. size=175635582, mt=1658258889.0 2025-07-24 16:53:32,297|caper.cromwell|INFO| Validating WDL/inputs/imports with Womtool... 2025-07-24 16:53:34,971|caper.nb_subproc_thread|INFO| Subprocess finished successfully. 2025-07-24 16:53:34,972|caper.cromwell|INFO| Passed Womtool validation. 2025-07-24 16:53:34,972|caper.caper_runner|INFO| launching run: wdl=/usr/local/ngseq/src/atac-seq-pipeline/atac.wdl, inputs=/scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut11_temp2429899/.caper_tmp/scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut11_temp2429899/atac.local.json, backend_conf=/scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut11_temp2429899/.caper_tmp/atac/20250724_164409_925369/backend.conf 2025-07-24 16:53:34,972|caper.cromwell|INFO| Installing Cromwell JAR... https://github.com/broadinstitute/cromwell/releases/download/82/cromwell-82.jar 2025-07-24 16:53:34,973|autouri.autouri|INFO| cp: (4f72526b) started. src=https://github.com/broadinstitute/cromwell/releases/download/82/cromwell-82.jar, dest=/home/trxcopy/.caper/cromwell_jar/cromwell-82.jar 2025-07-24 16:53:35,651|autouri.autouri|INFO| cp: (4f72526b) skipped due to name_size_match. size=253461816, mt=1658258802.0 2025-07-24 16:53:53,352|caper.cromwell_workflow_monitor|INFO| Workflow: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, status=Submitted 2025-07-24 16:53:53,394|caper.cromwell_workflow_monitor|INFO| Workflow: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, status=Running 2025-07-24 16:54:08,218|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.read_genome_tsv:-1, retry=0, status=Started, job_id=2432688 2025-07-24 16:54:08,224|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.read_genome_tsv:-1, retry=0, status=WaitingForReturnCode 2025-07-24 16:54:25,138|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.read_genome_tsv:-1, retry=0, status=Done 2025-07-24 16:54:33,119|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.align:0, retry=0, status=Started, job_id=2433183 2025-07-24 16:54:33,120|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.align:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:54:38,118|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.align_mito:0, retry=0, status=Started, job_id=2433361 2025-07-24 16:54:38,119|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.align_mito:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:54:53,496|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.align_mito:0, retry=0, status=Done 2025-07-24 16:55:47,587|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.align:0, retry=0, status=Done 2025-07-24 16:55:58,119|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.frac_mito:0, retry=0, status=Started, job_id=2435247 2025-07-24 16:55:58,120|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.filter_no_dedup:0, retry=0, status=Started, job_id=2435551 2025-07-24 16:55:58,120|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.frac_mito:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:55:58,121|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.filter_no_dedup:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:56:03,117|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.filter:0, retry=0, status=Started, job_id=2435800 2025-07-24 16:56:03,118|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.filter:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:56:03,966|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.frac_mito:0, retry=0, status=Done 2025-07-24 16:56:15,776|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.filter_no_dedup:0, retry=0, status=Done 2025-07-24 16:56:16,906|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.filter:0, retry=0, status=Done 2025-07-24 16:56:23,118|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.bam2ta_no_dedup:0, retry=0, status=Started, job_id=2436814 2025-07-24 16:56:23,119|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.bam2ta_no_dedup:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:56:28,123|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.bam2ta:0, retry=0, status=Started, job_id=2437261 2025-07-24 16:56:28,123|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.gc_bias:0, retry=0, status=Started, job_id=2438024 2025-07-24 16:56:28,124|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.fraglen_stat_pe:0, retry=0, status=Started, job_id=2437603 2025-07-24 16:56:28,124|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.fraglen_stat_pe:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:56:28,124|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.bam2ta:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:56:28,125|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.gc_bias:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:56:29,626|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.bam2ta_no_dedup:0, retry=0, status=Done 2025-07-24 16:56:32,555|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.bam2ta:0, retry=0, status=Done 2025-07-24 16:56:33,118|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.tss_enrich:0, retry=0, status=Started, job_id=2438342 2025-07-24 16:56:33,118|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.jsd:-1, retry=0, status=Started, job_id=2438655 2025-07-24 16:56:33,118|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.tss_enrich:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:56:33,119|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.jsd:-1, retry=0, status=WaitingForReturnCode 2025-07-24 16:56:38,117|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.xcor:0, retry=0, status=Started, job_id=2438992 2025-07-24 16:56:38,117|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.xcor:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:56:41,955|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.fraglen_stat_pe:0, retry=0, status=Done 2025-07-24 16:56:46,775|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.xcor:0, retry=0, status=Done 2025-07-24 16:56:48,120|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.macs2_signal_track:0, retry=0, status=Started, job_id=2440129 2025-07-24 16:56:48,120|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.call_peak:0, retry=0, status=Started, job_id=2439923 2025-07-24 16:56:48,120|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.annot_enrich:0, retry=0, status=Started, job_id=2439572 2025-07-24 16:56:48,120|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.annot_enrich:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:56:48,120|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.macs2_signal_track:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:56:48,120|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.call_peak:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:56:49,876|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.tss_enrich:0, retry=0, status=Done 2025-07-24 16:56:53,118|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.spr:0, retry=0, status=Started, job_id=2440314 2025-07-24 16:56:53,118|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.spr:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:56:56,696|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.spr:0, retry=0, status=Done 2025-07-24 16:56:59,825|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.jsd:-1, retry=0, status=Done 2025-07-24 16:57:08,119|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.call_peak_pr2:0, retry=0, status=Started, job_id=2440860 2025-07-24 16:57:08,119|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.call_peak_pr1:0, retry=0, status=Started, job_id=2440997 2025-07-24 16:57:08,119|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.call_peak_pr2:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:57:08,119|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.call_peak_pr1:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:57:08,316|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.annot_enrich:0, retry=0, status=Done 2025-07-24 16:59:16,706|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.gc_bias:0, retry=0, status=Done 2025-07-24 17:00:20,496|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.macs2_signal_track:0, retry=0, status=Done 2025-07-24 17:00:20,516|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.call_peak:0, retry=0, status=Done 2025-07-24 17:00:38,696|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.call_peak_pr2:0, retry=0, status=Done 2025-07-24 17:01:08,736|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.call_peak_pr1:0, retry=0, status=Done 2025-07-24 17:01:18,119|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.idr_pr:0, retry=0, status=Started, job_id=2444349 2025-07-24 17:01:18,119|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.idr_pr:0, retry=0, status=WaitingForReturnCode 2025-07-24 17:01:23,117|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.overlap_pr:0, retry=0, status=Started, job_id=2444498 2025-07-24 17:01:23,118|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.overlap_pr:0, retry=0, status=WaitingForReturnCode 2025-07-24 17:01:30,095|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.overlap_pr:0, retry=0, status=Done 2025-07-24 17:01:34,485|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.idr_pr:0, retry=0, status=Done 2025-07-24 17:01:38,118|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.reproducibility_overlap:-1, retry=0, status=Started, job_id=2444928 2025-07-24 17:01:38,118|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.reproducibility_overlap:-1, retry=0, status=WaitingForReturnCode 2025-07-24 17:01:43,117|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.reproducibility_idr:-1, retry=0, status=Started, job_id=2445074 2025-07-24 17:01:43,118|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.reproducibility_idr:-1, retry=0, status=WaitingForReturnCode 2025-07-24 17:01:48,946|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.reproducibility_overlap:-1, retry=0, status=Done 2025-07-24 17:01:49,466|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.reproducibility_idr:-1, retry=0, status=Done 2025-07-24 17:01:58,118|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.qc_report:-1, retry=0, status=Started, job_id=2445491 2025-07-24 17:01:58,118|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.qc_report:-1, retry=0, status=WaitingForReturnCode 2025-07-24 17:02:01,096|caper.cromwell_workflow_monitor|INFO| Task: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, task=atac.qc_report:-1, retry=0, status=Done 2025-07-24 17:02:08,145|caper.cromwell_workflow_monitor|INFO| Workflow: id=bbcc84ee-bf23-44a9-8709-5aee108757ea, status=Succeeded 2025-07-24 17:03:09,420|caper.cromwell_metadata|INFO| Wrote metadata file. /scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut11_temp2429899/atac/bbcc84ee-bf23-44a9-8709-5aee108757ea/metadata.json 2025-07-24 17:03:09,421|caper.nb_subproc_thread|INFO| Cromwell finished successfully. cp: will not overwrite just-created './qc.html' with './atac/bbcc84ee-bf23-44a9-8709-5aee108757ea/call-qc_report/execution/glob-eae855c82d0f7e2185388856e7b2cc7b/qc.html' cp: will not overwrite just-created './qc.json' with './atac/bbcc84ee-bf23-44a9-8709-5aee108757ea/call-qc_report/execution/glob-3440f922973abb7a616aaf203e0db08b/qc.json' ___STDERR_END___