/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/o35755_AtacENCODE_2025-07-24--16-43-39/scripts/QC_mut22_ventricles_100k_1.sh_sushiID1622_2025-07-24--16-43-50_o.log -------------------------------------------------- Job runs on fgcz-c-095 at /scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut22_temp2429898 Starting EzAppAtacENCODE AtacENCODE o35755_AtacENCODE_2025-07-24--16-43-39_mut22_temp2429898 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_mut22_temp2429898 2025-07-24 17:01:55 [1] "Success" ___STDOUT_END___ /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/o35755_AtacENCODE_2025-07-24--16-43-39/scripts/QC_mut22_ventricles_100k_1.sh_sushiID1622_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_mut22_temp2429898/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_mut22_temp2429898/.caper_tmp/atac/20250724_164409_925225 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_mut22_temp2429898/.caper_tmp/atac/20250724_164409_925225 2025-07-24 16:44:10,127|autouri.autouri|INFO| cp: (f90031c8) 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_mut22_temp2429898/.caper_tmp/72041e824adb499a4974d85ba31fe30d/mm10_no_alt_analysis_set_ENCODE.fasta.gz 2025-07-24 16:45:00,762|autouri.autouri|INFO| cp: (f90031c8) done. 2025-07-24 16:45:00,764|autouri.autouri|INFO| cp: (2a18fb2d) 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_mut22_temp2429898/.caper_tmp/bbf176bc384fbe2a734ff0122b8315b3/mm10_no_alt_analysis_set_ENCODE_mito_only.fasta.gz 2025-07-24 16:45:02,066|autouri.autouri|INFO| cp: (2a18fb2d) done. 2025-07-24 16:45:02,067|autouri.autouri|INFO| cp: (d3a872df) started. src=https://www.encodeproject.org/files/ENCFF547MET/@@download/ENCFF547MET.bed.gz, dest=/scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut22_temp2429898/.caper_tmp/da42a1c4b0f9d3225600da56b2c9571d/ENCFF547MET.bed.gz 2025-07-24 16:45:03,320|autouri.autouri|INFO| cp: (d3a872df) done. 2025-07-24 16:45:04,602|autouri.autouri|INFO| cp: (3d299b2c) 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_mut22_temp2429898/.caper_tmp/a4733a4e097a19c869b1cb1aae1b33c9/mm10_no_alt.chrom.sizes.tsv 2025-07-24 16:45:05,886|autouri.autouri|INFO| cp: (3d299b2c) done. 2025-07-24 16:45:05,887|autouri.autouri|INFO| cp: (f9e57a99) started. src=https://www.encodeproject.org/files/ENCFF309GLL/@@download/ENCFF309GLL.tar.gz, dest=/scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut22_temp2429898/.caper_tmp/042925a7d9816ca478718df2aee1b980/ENCFF309GLL.tar.gz 2025-07-24 16:48:30,029|autouri.autouri|INFO| cp: (f9e57a99) done. 2025-07-24 16:48:30,030|autouri.autouri|INFO| cp: (bee04299) 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_mut22_temp2429898/.caper_tmp/820a6f4379a41332ddf3f25fc09101d5/mm10_no_alt_analysis_set_ENCODE_mito_only_bowtie2_index.tar.gz 2025-07-24 16:48:31,807|autouri.autouri|INFO| cp: (bee04299) done. 2025-07-24 16:48:31,808|autouri.autouri|INFO| cp: (8665ba38) started. src=https://www.encodeproject.org/files/ENCFF018NEO/@@download/ENCFF018NEO.tar.gz, dest=/scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut22_temp2429898/.caper_tmp/506b880ea82aeae31802ecd4b265cff9/ENCFF018NEO.tar.gz 2025-07-24 16:52:26,787|autouri.autouri|INFO| cp: (8665ba38) done. 2025-07-24 16:52:26,789|autouri.autouri|INFO| cp: (398fcf87) 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_mut22_temp2429898/.caper_tmp/4ce6df75b5bc0d2c95fb08049d00b722/mm10_no_alt_analysis_set_ENCODE_mito_only_bwa_index.tar.gz 2025-07-24 16:52:28,168|autouri.autouri|INFO| cp: (398fcf87) done. 2025-07-24 16:52:28,169|autouri.autouri|INFO| cp: (5c4e8daa) started. src=https://www.encodeproject.org/files/ENCFF454VOL/@@download/ENCFF454VOL.bed.gz, dest=/scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut22_temp2429898/.caper_tmp/4d2e30a0649d95b154163e7017f0b76c/ENCFF454VOL.bed.gz 2025-07-24 16:52:30,009|autouri.autouri|INFO| cp: (5c4e8daa) done. 2025-07-24 16:52:30,010|autouri.autouri|INFO| cp: (4196d6f9) started. src=https://www.encodeproject.org/files/ENCFF015KVI/@@download/ENCFF015KVI.bed.gz, dest=/scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut22_temp2429898/.caper_tmp/b7f1373597857ea4d8a11c3915c4455d/ENCFF015KVI.bed.gz 2025-07-24 16:52:33,781|autouri.autouri|INFO| cp: (4196d6f9) done. 2025-07-24 16:52:33,782|autouri.autouri|INFO| cp: (b255eaff) started. src=https://www.encodeproject.org/files/ENCFF206BQS/@@download/ENCFF206BQS.bed.gz, dest=/scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut22_temp2429898/.caper_tmp/571f676aa2f98f5bffdb06c91453cffd/ENCFF206BQS.bed.gz 2025-07-24 16:52:35,477|autouri.autouri|INFO| cp: (b255eaff) done. 2025-07-24 16:52:35,477|autouri.autouri|INFO| cp: (5bc321d1) started. src=https://www.encodeproject.org/files/ENCFF580RGZ/@@download/ENCFF580RGZ.bed.gz, dest=/scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut22_temp2429898/.caper_tmp/799bb08d7265d45d0a81bd65d6b7c7f0/ENCFF580RGZ.bed.gz 2025-07-24 16:52:39,076|autouri.autouri|INFO| cp: (5bc321d1) done. 2025-07-24 16:52:39,077|autouri.autouri|INFO| cp: (03216e95) 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_mut22_temp2429898/.caper_tmp/cf2b604559fb2950d79aa439cafa86d0/mm10_dnase_avg_fseq_signal_formatted.txt.gz 2025-07-24 16:52:40,392|autouri.autouri|INFO| cp: (03216e95) done. 2025-07-24 16:52:40,393|autouri.autouri|INFO| cp: (2833b9d7) 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_mut22_temp2429898/.caper_tmp/6cb5db6af37a5741fb86a6a9bf21f3f1/mm10_celltype_compare_subsample.bed.gz 2025-07-24 16:52:41,144|autouri.autouri|INFO| cp: (2833b9d7) done. 2025-07-24 16:52:41,145|autouri.autouri|INFO| cp: (7d095902) 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_mut22_temp2429898/.caper_tmp/fe37c3c5d22dfa5e5b26520a3ba8ac8f/mm10_dnase_avg_fseq_signal_metadata.txt 2025-07-24 16:52:41,326|autouri.autouri|INFO| cp: (7d095902) done. 2025-07-24 16:52:42,093|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 16:52:42,147|caper.cromwell|INFO| Installing Womtool JAR... https://github.com/broadinstitute/cromwell/releases/download/82/womtool-82.jar 2025-07-24 16:52:42,148|autouri.autouri|INFO| cp: (0b2dfd49) 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 16:52:44,662|autouri.autouri|INFO| cp: (0b2dfd49) skipped due to name_size_match. size=175635582, mt=1658258889.0 2025-07-24 16:52:44,668|caper.cromwell|INFO| Validating WDL/inputs/imports with Womtool... 2025-07-24 16:52:47,789|caper.nb_subproc_thread|INFO| Subprocess finished successfully. 2025-07-24 16:52:47,789|caper.cromwell|INFO| Passed Womtool validation. 2025-07-24 16:52:47,789|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_mut22_temp2429898/.caper_tmp/scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut22_temp2429898/atac.local.json, backend_conf=/scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut22_temp2429898/.caper_tmp/atac/20250724_164409_925225/backend.conf 2025-07-24 16:52:47,790|caper.cromwell|INFO| Installing Cromwell JAR... https://github.com/broadinstitute/cromwell/releases/download/82/cromwell-82.jar 2025-07-24 16:52:47,790|autouri.autouri|INFO| cp: (15d776aa) 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 16:52:51,113|autouri.autouri|INFO| cp: (15d776aa) skipped due to name_size_match. size=253461816, mt=1658258802.0 2025-07-24 16:53:08,637|caper.cromwell_workflow_monitor|INFO| Workflow: id=b6d87363-d68d-4cbd-836c-b8ac42756695, status=Submitted 2025-07-24 16:53:08,650|caper.cromwell_workflow_monitor|INFO| Workflow: id=b6d87363-d68d-4cbd-836c-b8ac42756695, status=Running 2025-07-24 16:53:23,429|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.read_genome_tsv:-1, retry=0, status=Started, job_id=2431686 2025-07-24 16:53:23,434|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.read_genome_tsv:-1, retry=0, status=WaitingForReturnCode 2025-07-24 16:54:25,335|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.read_genome_tsv:-1, retry=0, status=Done 2025-07-24 16:54:33,414|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.align:0, retry=0, status=Started, job_id=2433275 2025-07-24 16:54:33,415|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.align:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:54:38,414|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.align_mito:0, retry=0, status=Started, job_id=2433558 2025-07-24 16:54:38,414|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.align_mito:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:54:54,032|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.align_mito:0, retry=0, status=Done 2025-07-24 16:55:42,942|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.align:0, retry=0, status=Done 2025-07-24 16:55:53,414|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.frac_mito:0, retry=0, status=Started, job_id=2434913 2025-07-24 16:55:53,414|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.filter:0, retry=0, status=Started, job_id=2435046 2025-07-24 16:55:53,415|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.frac_mito:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:55:53,415|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.filter:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:55:58,415|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.filter_no_dedup:0, retry=0, status=Started, job_id=2435203 2025-07-24 16:55:58,415|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.filter_no_dedup:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:55:59,772|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.frac_mito:0, retry=0, status=Done 2025-07-24 16:56:11,311|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.filter:0, retry=0, status=Done 2025-07-24 16:56:13,091|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.filter_no_dedup:0, retry=0, status=Done 2025-07-24 16:56:18,414|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.bam2ta_no_dedup:0, retry=0, status=Started, job_id=2436626 2025-07-24 16:56:18,414|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.bam2ta_no_dedup:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:56:23,415|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.gc_bias:0, retry=0, status=Started, job_id=2436758 2025-07-24 16:56:23,415|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.fraglen_stat_pe:0, retry=0, status=Started, job_id=2437003 2025-07-24 16:56:23,415|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.bam2ta:0, retry=0, status=Started, job_id=2437203 2025-07-24 16:56:23,416|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.gc_bias:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:56:23,416|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.bam2ta:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:56:23,416|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.fraglen_stat_pe:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:56:25,471|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.bam2ta_no_dedup:0, retry=0, status=Done 2025-07-24 16:56:28,424|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.jsd:-1, retry=0, status=Started, job_id=2437864 2025-07-24 16:56:28,424|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.tss_enrich:0, retry=0, status=Started, job_id=2437484 2025-07-24 16:56:28,425|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.tss_enrich:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:56:28,425|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.jsd:-1, retry=0, status=WaitingForReturnCode 2025-07-24 16:56:31,471|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.bam2ta:0, retry=0, status=Done 2025-07-24 16:56:33,413|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.xcor:0, retry=0, status=Started, job_id=2438222 2025-07-24 16:56:33,413|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.xcor:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:56:38,971|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.fraglen_stat_pe:0, retry=0, status=Done 2025-07-24 16:56:40,731|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.xcor:0, retry=0, status=Done 2025-07-24 16:56:43,414|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.annot_enrich:0, retry=0, status=Started, job_id=2439186 2025-07-24 16:56:43,414|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.spr:0, retry=0, status=Started, job_id=2439517 2025-07-24 16:56:43,415|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.call_peak:0, retry=0, status=Started, job_id=2439384 2025-07-24 16:56:43,415|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.annot_enrich:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:56:43,415|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.spr:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:56:43,415|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.call_peak:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:56:48,413|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.macs2_signal_track:0, retry=0, status=Started, job_id=2439756 2025-07-24 16:56:48,413|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.macs2_signal_track:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:56:49,631|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.tss_enrich:0, retry=0, status=Done 2025-07-24 16:56:52,012|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.spr:0, retry=0, status=Done 2025-07-24 16:56:56,812|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.jsd:-1, retry=0, status=Done 2025-07-24 16:57:02,102|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.annot_enrich:0, retry=0, status=Done 2025-07-24 16:57:03,414|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.call_peak_pr1:0, retry=0, status=Started, job_id=2440581 2025-07-24 16:57:03,414|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.call_peak_pr2:0, retry=0, status=Started, job_id=2440729 2025-07-24 16:57:03,414|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.call_peak_pr2:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:57:03,414|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.call_peak_pr1:0, retry=0, status=WaitingForReturnCode 2025-07-24 16:59:08,832|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.gc_bias:0, retry=0, status=Done 2025-07-24 16:59:59,191|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.macs2_signal_track:0, retry=0, status=Done 2025-07-24 17:00:02,231|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.call_peak:0, retry=0, status=Done 2025-07-24 17:00:13,951|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.call_peak_pr2:0, retry=0, status=Done 2025-07-24 17:00:20,241|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.call_peak_pr1:0, retry=0, status=Done 2025-07-24 17:00:28,414|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.idr_pr:0, retry=0, status=Started, job_id=2443055 2025-07-24 17:00:28,415|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.idr_pr:0, retry=0, status=WaitingForReturnCode 2025-07-24 17:00:33,413|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.overlap_pr:0, retry=0, status=Started, job_id=2443145 2025-07-24 17:00:33,413|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.overlap_pr:0, retry=0, status=WaitingForReturnCode 2025-07-24 17:00:37,442|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.overlap_pr:0, retry=0, status=Done 2025-07-24 17:00:43,413|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.reproducibility_overlap:-1, retry=0, status=Started, job_id=2443625 2025-07-24 17:00:43,413|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.reproducibility_overlap:-1, retry=0, status=WaitingForReturnCode 2025-07-24 17:00:46,911|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.idr_pr:0, retry=0, status=Done 2025-07-24 17:00:53,413|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.reproducibility_idr:-1, retry=0, status=Started, job_id=2443904 2025-07-24 17:00:53,413|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.reproducibility_idr:-1, retry=0, status=WaitingForReturnCode 2025-07-24 17:00:53,692|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.reproducibility_overlap:-1, retry=0, status=Done 2025-07-24 17:01:02,151|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.reproducibility_idr:-1, retry=0, status=Done 2025-07-24 17:01:08,413|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.qc_report:-1, retry=0, status=Started, job_id=2444186 2025-07-24 17:01:08,414|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.qc_report:-1, retry=0, status=WaitingForReturnCode 2025-07-24 17:01:14,671|caper.cromwell_workflow_monitor|INFO| Task: id=b6d87363-d68d-4cbd-836c-b8ac42756695, task=atac.qc_report:-1, retry=0, status=Done 2025-07-24 17:01:23,442|caper.cromwell_workflow_monitor|INFO| Workflow: id=b6d87363-d68d-4cbd-836c-b8ac42756695, status=Succeeded 2025-07-24 17:01:54,704|caper.cromwell_metadata|INFO| Wrote metadata file. /scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut22_temp2429898/atac/b6d87363-d68d-4cbd-836c-b8ac42756695/metadata.json 2025-07-24 17:01:54,704|caper.nb_subproc_thread|INFO| Cromwell finished successfully. cp: will not overwrite just-created './qc.html' with './atac/b6d87363-d68d-4cbd-836c-b8ac42756695/call-qc_report/execution/glob-eae855c82d0f7e2185388856e7b2cc7b/qc.html' cp: will not overwrite just-created './qc.json' with './atac/b6d87363-d68d-4cbd-836c-b8ac42756695/call-qc_report/execution/glob-3440f922973abb7a616aaf203e0db08b/qc.json' ___STDERR_END___