Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/hrd_score_altera_bam/dbsnp_baseline_altera.260120.tsv.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/3aa5beff1716522d35b0ee675d3ff2/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/a886d13c5e1c109b5dc44a9106650e/HCC1395_tumor_vs_HCC1395_BL.vcf.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-2d63fc3d-bead-4e15-85fc-b81dc24b0797/ce/9964b9139b61be8be314b28cce6fbc/hrd_score_altera_bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/a886d13c5e1c109b5dc44a9106650e/HCC1395_tumor_vs_HCC1395_BL.vcf.gz.tbi
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/3aa5beff1716522d35b0ee675d3ff2/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/21/24929ee038540aa06bce4b7daeaaca/HCC1395_tumor_vs_HCC1395_BL.pileup.csv.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-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.WZnTVeBR3M/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':
write
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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combine, intersect, setdiff, union
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IQR, mad, sd, var, xtabs
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Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
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: IRanges
Attaching package: 'IRanges'
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collapse, desc, slice
Loading required package: GenomeInfoDb
Loading required package: NMF
Loading required package: pkgmaker
Loading required package: registry
Attaching package: 'pkgmaker'
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new2
Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: bigmemory] | Cores 383/384
To enable shared memory capabilities, try: install.extras('
NMF
')
Attaching package: 'NMF'
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nrun
Attaching package: 'data.table'
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first, second
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between, first, last
Loading required package: gridExtra
Attaching package: 'gridExtra'
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combine
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combine
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combine
Attaching package: 'purrr'
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transpose
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reduce
The following object is masked from 'package:IRanges':
reduce
Tumor bam =
Normal bam =
FACETS pileup = HCC1395_tumor_vs_HCC1395_BL.pileup.csv.gz
Bypass segments =
Bypass ploidy =
Somatic vcf = HCC1395_tumor_vs_HCC1395_BL.vcf.gz
Starting from: pileup
Taking input= as a system command because it contains a space ('gunzip -c dbsnp_baseline_altera.260120.tsv.gz'). If it's a filename please remove the space, or use file= explicitly. A variable is being passed to input= and when this is taken as a system command there is a security concern if you are creating an app, the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Taking input= as a system command because it contains a space ('gunzip -c HCC1395_tumor_vs_HCC1395_BL.pileup.csv.gz'). If it's a filename please remove the space, or use file= explicitly. A variable is being passed to input= and when this is taken as a system command there is a security concern if you are creating an app, the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Writing to ./FACETS
Fontconfig warning: using without calling FcInit()
Fontconfig error: No writable cache directories
/opt/conda/envs/env_tih_hrd_running_env/var/cache/fontconfig
/.cache/fontconfig
/.fontconfig
Attaching package: 'XVector'
The following object is masked from 'package:purrr':
compact
Attaching package: 'Biostrings'
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strsplit
Attaching package: 'rtracklayer'
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FileForFormat
Skipping CNV signatures ploidy adjustment (adjust_ploidy = FALSE or not set)
QC status: review (score=70, issues: Extreme |dipLogR| (>0.35): possible baseline mis-centering)
Writing ./HCC1395_tumor_vs_HCC1395_BL.hrd_score_results.tsv
COMPLETE HRDscore