Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_tumor/HCC1395_tumor.recalibrated.bam.bai Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/ce1dfdc69ea6fb70a1e55b9dab3d85/.command.sh Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_tumor/HCC1395_tumor.recalibrated.bam Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_BL/HCC1395_BL.recalibrated.bam Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_BL/HCC1395_BL.recalibrated.bam.bai Downloading: s3://natera-platform-sandbox/pipeline-resources/ensembl/Homo_sapiens.GRCh38.110.gtf.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/ce1dfdc69ea6fb70a1e55b9dab3d85/.command.run Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz ==> STAGING COMPLETE (9 inputs) [W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi [W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi [W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai Finished in 3.974314 seconds. [W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi [W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai Finished in 4.392995 seconds. [W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi [W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai Finished in 3.590332 seconds. [W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi [W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai Finished in 3.442098 seconds. 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[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi [W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai Finished in 2.908990 seconds. [W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi [W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai Finished in 2.393751 seconds. [W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi [W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai Finished in 2.663796 seconds. 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[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi [W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai Finished in 1.923088 seconds. [W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi [W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai Finished in 1.929649 seconds. [W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi [W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai Finished in 2.047753 seconds. [W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi [W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai Finished in 1.931299 seconds. [W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi [W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai Finished in 1.703373 seconds. [W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi [W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai Finished in 1.584637 seconds. 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[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi [W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai Finished in 2.169555 seconds. [W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi [W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai Finished in 0.144915 seconds. [W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi [W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai Finished in 0.003003 seconds. [2026-06-09 03:08:09.916408] Loading file HCC1395_tumor_vs_HCC1395_BL.pileup.csv.gz... [2026-06-09 03:08:10.64791] Plotting histogram of coverage... [1] "Writing bt_model_coefs and gc_model_coefs." [2026-06-09 03:08:16.786644] Preprocessing sample... [2026-06-09 03:08:17.175534] Processing sample... [2026-06-09 03:08:17.206746] Fitting model... [2026-06-09 03:08:42.781799] Writing output [1] "Writing facets jointseg csv" [1] "Writing facets gene_cncf csv" [1] "Writing facets cncf segments csv" [1] "Writing purity, ploidy, and dipLogR." [2026-06-09 03:08:42.942352] Plotting genome... Fontconfig error: No writable cache directories [2026-06-09 03:08:43.099724] Plotting spider... R version 4.3.3 (2024-02-29) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default BLAS/LAPACK: /opt/conda/envs/env_facets/lib/libopenblasp-r0.3.30.so; LAPACK version 3.12.0 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: Etc/UTC tzcode source: system (glibc) attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] gridExtra_2.3 ggplot2_3.5.2 Rsamtools_2.18.0 [4] Biostrings_2.70.1 XVector_0.42.0 GenomicRanges_1.54.1 [7] GenomeInfoDb_1.38.1 IRanges_2.36.0 S4Vectors_0.40.2 [10] BiocGenerics_0.48.1 data.table_1.17.8 facets_0.6.2 [13] pctGCdata_0.3.0 argparse_2.2.5 loaded via a namespace (and not attached): [1] jsonlite_2.0.0 gtable_0.3.6 dplyr_1.1.4 [4] compiler_4.3.3 crayon_1.5.3 tidyselect_1.2.1 [7] bitops_1.0-9 textshaping_1.0.3 systemfonts_1.2.3 [10] scales_1.4.0 BiocParallel_1.36.0 R6_2.6.1 [13] labeling_0.4.3 generics_0.1.4 tibble_3.3.0 [16] GenomeInfoDbData_1.2.11 findpython_1.0.9 pillar_1.11.0 [19] RColorBrewer_1.1-3 rlang_1.1.6 cli_3.6.5 [22] withr_3.0.2 magrittr_2.0.3 zlibbioc_1.48.0 [25] grid_4.3.3 lifecycle_1.0.4 vctrs_0.6.5 [28] glue_1.8.0 farver_2.1.2 ragg_1.5.0 [31] codetools_0.2-20 RCurl_1.98-1.17 tools_4.3.3 [34] pkgconfig_2.0.3 Warning message: In data.table::fread(cmd = paste("zcat", gtf_file), col.names = std_cols) : Detected 1 column names but the data has 9 columns (i.e. invalid file). Added 8 extra default column names at the end.