Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/bf6cdb3ec3c2cfa7ec500bdf8f5c2e/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/5f3612523c5a831477f17d4aee1b22/custom_Sig_18_tumor_normal.vcf.gz.tbi
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-1bd6f233-9a0b-4b84-8acd-4ee72930a4e8/f2/da7bb6b09a5ed3ab9504a81b45b71a/hrd_score_altera_bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/5db4c32d6248579a9b8f0623773fe7/custom_Sig_18_tumor_normal.segments.csv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/5db4c32d6248579a9b8f0623773fe7/custom_Sig_18_tumor_normal.purity_ploidy.csv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/bf6cdb3ec3c2cfa7ec500bdf8f5c2e/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/5f3612523c5a831477f17d4aee1b22/custom_Sig_18_tumor_normal.vcf.gz
==> STAGING COMPLETE (7 inputs)
* installing *source* package 'HRDscoreAlteraBam' ...
** using staged installation
** libs
using C compiler: 'x86_64-conda-linux-gnu-cc (conda-forge gcc 15.2.0-18) 15.2.0'
using Fortran compiler: 'GNU Fortran (conda-forge gcc 15.2.0-18) 15.2.0'
x86_64-conda-linux-gnu-cc -I"/opt/conda/envs/env_tih_hrd_running_env/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/envs/env_tih_hrd_running_env/include -I/opt/conda/envs/env_tih_hrd_running_env/include -Wl,-rpath-link,/opt/conda/envs/env_tih_hrd_running_env/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/envs/env_tih_hrd_running_env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1763744062972/work=/usr/local/src/conda/r-base-4.3.3 -fdebug-prefix-map=/opt/conda/envs/env_tih_hrd_running_env=/usr/local/src/conda-prefix -c 000.init.c -o 000.init.o
x86_64-conda-linux-gnu-gfortran -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/envs/env_tih_hrd_running_env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1763744062972/work=/usr/local/src/conda/r-base-4.3.3 -fdebug-prefix-map=/opt/conda/envs/env_tih_hrd_running_env=/usr/local/src/conda-prefix -c scansnp-random.f -o scansnp-random.o
x86_64-conda-linux-gnu-cc -shared -L/opt/conda/envs/env_tih_hrd_running_env/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/envs/env_tih_hrd_running_env/lib -Wl,-rpath-link,/opt/conda/envs/env_tih_hrd_running_env/lib -L/opt/conda/envs/env_tih_hrd_running_env/lib -o HRDscoreAlteraBam.so 000.init.o cbs2rank.o rshared.o scansnp-random.o -lgfortran -lm -lquadmath -L/opt/conda/envs/env_tih_hrd_running_env/lib/R/lib -lR
installing to /tmp/nxf.fBtGEY7Ods/R_libs/00LOCK-hrd_score_altera_bam/00new/HRDscoreAlteraBam/libs
** R
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package 'HRDscoreAlteraBam'
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HRDscoreAlteraBam)
Loading required package: pctGCdata
Attaching package: 'HRDscoreAlteraBam'
The following object is masked from 'package:base':
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Attaching package: 'dplyr'
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Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
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Loading required package: GenomeInfoDb
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Attaching package: 'pkgmaker'
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Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: bigmemory] | Cores 191/192
To enable shared memory capabilities, try: install.extras('
NMF
')
Attaching package: 'NMF'
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Attaching package: 'data.table'
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Loading required package: gridExtra
Attaching package: 'gridExtra'
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Attaching package: 'purrr'
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Tumor bam =
Normal bam =
FACETS pileup =
Bypass segments = custom_Sig_18_tumor_normal.segments.csv
Bypass ploidy = custom_Sig_18_tumor_normal.purity_ploidy.csv
Somatic vcf = custom_Sig_18_tumor_normal.vcf.gz
Starting from: bypass
Bypassing FACETS processing and using provided segments and ploidy files.
Attaching package: 'XVector'
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Attaching package: 'Biostrings'
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Attaching package: 'rtracklayer'
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FileForFormat
Skipping CNV signatures ploidy adjustment (adjust_ploidy = FALSE or not set)
QC status: poor (score=NA, issues: Missing dipLogR, purity, or ploidy)
Writing ./custom_Sig_18_tumor_normal.hrd_score_results.tsv
COMPLETE HRDscore