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-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-rnd-pltf-dev-nextflow-scratch-01/work/f3/4d4021855ab7665413fbdde63cc3a2/.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_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/f3/4d4021855ab7665413fbdde63cc3a2/.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)
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Finished in 1.467285 seconds.
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Finished in 16.466318 seconds.
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Finished in 0.153353 seconds.
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Finished in 0.003128 seconds.
[2026-06-08 20:37:23.021864] Loading file HCC1395_tumor_vs_HCC1395_BL.pileup.csv.gz...
[2026-06-08 20:37:23.802241] Plotting histogram of coverage...
[1] "Writing bt_model_coefs and gc_model_coefs."
[2026-06-08 20:37:30.020944] Preprocessing sample...
[2026-06-08 20:37:30.398473] Processing sample...
[2026-06-08 20:37:30.42924] Fitting model...
[2026-06-08 20:37:54.999457] 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."
[2026-06-08 20:37:55.143501] Plotting genome...
Fontconfig error: No writable cache directories
[2026-06-08 20:37:55.298765] 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.