Running SomaticSniper-Battenberg-DPClust single-region mode worked fine. Same issue for Strelka2/Mutect2-Battenberg-DPClust-mr. Could this be do to the naming conventions in multi-region mode?
ERRRORING:
example error log:/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-somaticsniper-battenberg-dpclust/logs/ILHNLNEV000001_51404_SomaticSniper-Battenberg-DPClust-mr.log
error message:
Error executing process > 'workflow_dpclust:call_RunDP_DPClust'
Caused by:
Process `workflow_dpclust:call_RunDP_DPClust` terminated with an error exit status (1)
Command executed:
set -euo pipefail
printf "ILHNLNEV000001 ILHNLNEV000001-T001-P01-F ILHNLNEV000001-T001-P01-F_allDirichletProcessInfo.txt 0.562956521739133 male NA NA
ILHNLNEV000001 ILHNLNEV000001-T002-P02-F ILHNLNEV000001-T002-P02-F_allDirichletProcessInfo.txt 0.534937500000003 male NA NA
ILHNLNEV000001 ILHNLNEV000001-T004-L02-F ILHNLNEV000001-T004-L02-F_allDirichletProcessInfo.txt 0.56375 male NA NA
ILHNLNEV000001 ILHNLNEV000001-T003-L01-F ILHNLNEV000001-T003-L01-F_allDirichletProcessInfo.txt 0.635411764705883 male NA NA\n" > ILHNLNEV000001_project_file_intermediate.txt
printf "sample\tsubsample\tdatafile\tcellularity\tsex\tcnadatafile\tindeldatafile\n" > ILHNLNEV000001_project_file.txt
while IFS=$' ' read -r -a arr
do
printf "${arr[0]} ${arr[1]} `realpath ${arr[2]}` ${arr[3]} ${arr[4]} ${arr[5]} ${arr[6]}
" >> ILHNLNEV000001_project_file.txt
done < ILHNLNEV000001_project_file_intermediate.txt
Rscript /hot/user/yashpatel/pipeline-call-SRC/pipeline-call-SRC/./module/dpclust_pipeline.R -d / -o ./ -r 1 -i ILHNLNEV000001_project_file.txt -k --seed 51404 --min_frac_muts_cluster -1
Command exit status:
1
Command output:
[1] ""
[1] "Running: ILHNLNEV000001"
[1] "Working dir: ./"
[1] "Analysis type: nd_dp"
[1] "Datafiles:"
[1] "/scratch/a5/6366225258c0ad8a129d3ec010786d/ILHNLNEV000001-T001-P01-F_allDirichletProcessInfo.txt"
[2] "/scratch/d7/a532ec8d496ea3341b9870422ef64e/ILHNLNEV000001-T002-P02-F_allDirichletProcessInfo.txt"
[3] "/scratch/eb/a2e279c6532a1d09f610ce9f169057/ILHNLNEV000001-T004-L02-F_allDirichletProcessInfo.txt"
[4] "/scratch/1d/dfcbeab28d7f14aa8ba183989389bd/ILHNLNEV000001-T003-L01-F_allDirichletProcessInfo.txt"
[1] ""
[1] "Loading data..."
Command error:
Bioconductor version 3.12 (BiocManager 1.30.10), ?BiocManager::install for help
Bioconductor version '3.12' is out-of-date; the current release version '3.16'
is available with R version '4.2'; see https://bioconductor.org/install
[1] ""
[1] "Running: ILHNLNEV000001"
[1] "Working dir: ./"
[1] "Analysis type: nd_dp"
[1] "Datafiles:"
[1] "/scratch/a5/6366225258c0ad8a129d3ec010786d/ILHNLNEV000001-T001-P01-F_allDirichletProcessInfo.txt"
[2] "/scratch/d7/a532ec8d496ea3341b9870422ef64e/ILHNLNEV000001-T002-P02-F_allDirichletProcessInfo.txt"
[3] "/scratch/eb/a2e279c6532a1d09f610ce9f169057/ILHNLNEV000001-T004-L02-F_allDirichletProcessInfo.txt"
[4] "/scratch/1d/dfcbeab28d7f14aa8ba183989389bd/ILHNLNEV000001-T003-L01-F_allDirichletProcessInfo.txt"
[1] ""
The following objects are masked _by_ .GlobalEnv:
assign_sampled_muts, generate_cluster_ordering, keep_temp_files,
min_frac_muts_cluster, min_muts_cluster, mut.assignment.type,
no.iters, no.iters.burn.in, num_muts_sample, species
The following objects are masked _by_ .GlobalEnv:
cellularity, datafiles, is.male, mutphasingfiles, samplename,
subsamples
The following object is masked _by_ .GlobalEnv:
seed
[1] "Loading data..."
Error in chromosome[, s] <- list_of_tables[[s]][, Chromosome] :
number of items to replace is not a multiple of replacement length
Calls: RunDP -> load.data -> load.data.inner
Execution halted
Work dir:
/scratch/e3/cf0259876c1768a25ea46be8f5c564
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
executor > local (18)
[81/6500d0] process > run_validate_PipeVal (1) [100%] 12 of 12 ✔
[3c/5786d4] process > create_inputs_SRCutil (1) [100%] 1 of 1 ✔
[- ] process > workflow_pyclonevi:fit_mode... -
[- ] process > workflow_pyclonevi:write_re... -
[- ] process > workflow_phylowgs:call_mult... -
[- ] process > workflow_phylowgs:write_res... -
[- ] process > workflow_phylowgs:index_dat... -
[1d/dfcbea] process > workflow_dpclust:generate_i... [100%] 4 of 4 ✔
[e3/cf0259] process > workflow_dpclust:call_RunDP... [100%] 1 of 1, failed: 1 ✘
[- ] process > workflow_pyclone:run_analys... -
[- ] process > workflow_fastclone:run_solv... -
Error executing process > 'workflow_dpclust:call_RunDP_DPClust'
Caused by:
Process `workflow_dpclust:call_RunDP_DPClust` terminated with an error exit status (1)
Command executed:
set -euo pipefail
printf "ILHNLNEV000001 ILHNLNEV000001-T001-P01-F ILHNLNEV000001-T001-P01-F_allDirichletProcessInfo.txt 0.562956521739133 male NA NA
ILHNLNEV000001 ILHNLNEV000001-T002-P02-F ILHNLNEV000001-T002-P02-F_allDirichletProcessInfo.txt 0.534937500000003 male NA NA
ILHNLNEV000001 ILHNLNEV000001-T004-L02-F ILHNLNEV000001-T004-L02-F_allDirichletProcessInfo.txt 0.56375 male NA NA
ILHNLNEV000001 ILHNLNEV000001-T003-L01-F ILHNLNEV000001-T003-L01-F_allDirichletProcessInfo.txt 0.635411764705883 male NA NA\n" > ILHNLNEV000001_project_file_intermediate.txt
printf "sample\tsubsample\tdatafile\tcellularity\tsex\tcnadatafile\tindeldatafile\n" > ILHNLNEV000001_project_file.txt
while IFS=$' ' read -r -a arr
do
printf "${arr[0]} ${arr[1]} `realpath ${arr[2]}` ${arr[3]} ${arr[4]} ${arr[5]} ${arr[6]}
" >> ILHNLNEV000001_project_file.txt
done < ILHNLNEV000001_project_file_intermediate.txt
Rscript /hot/user/yashpatel/pipeline-call-SRC/pipeline-call-SRC/./module/dpclust_pipeline.R -d / -o ./ -r 1 -i ILHNLNEV000001_project_file.txt -k --seed 51404 --min_frac_muts_cluster -1
Command exit status:
1
Command output:
[1] ""
[1] "Running: ILHNLNEV000001"
[1] "Working dir: ./"
[1] "Analysis type: nd_dp"
[1] "Datafiles:"
[1] "/scratch/a5/6366225258c0ad8a129d3ec010786d/ILHNLNEV000001-T001-P01-F_allDirichletProcessInfo.txt"
[2] "/scratch/d7/a532ec8d496ea3341b9870422ef64e/ILHNLNEV000001-T002-P02-F_allDirichletProcessInfo.txt"
[3] "/scratch/eb/a2e279c6532a1d09f610ce9f169057/ILHNLNEV000001-T004-L02-F_allDirichletProcessInfo.txt"
[4] "/scratch/1d/dfcbeab28d7f14aa8ba183989389bd/ILHNLNEV000001-T003-L01-F_allDirichletProcessInfo.txt"
[1] ""
[1] "Loading data..."
Command error:
Bioconductor version 3.12 (BiocManager 1.30.10), ?BiocManager::install for help
Bioconductor version '3.12' is out-of-date; the current release version '3.16'
is available with R version '4.2'; see https://bioconductor.org/install
[1] ""
[1] "Running: ILHNLNEV000001"
[1] "Working dir: ./"
[1] "Analysis type: nd_dp"
[1] "Datafiles:"
[1] "/scratch/a5/6366225258c0ad8a129d3ec010786d/ILHNLNEV000001-T001-P01-F_allDirichletProcessInfo.txt"
[2] "/scratch/d7/a532ec8d496ea3341b9870422ef64e/ILHNLNEV000001-T002-P02-F_allDirichletProcessInfo.txt"
[3] "/scratch/eb/a2e279c6532a1d09f610ce9f169057/ILHNLNEV000001-T004-L02-F_allDirichletProcessInfo.txt"
[4] "/scratch/1d/dfcbeab28d7f14aa8ba183989389bd/ILHNLNEV000001-T003-L01-F_allDirichletProcessInfo.txt"
[1] ""
The following objects are masked _by_ .GlobalEnv:
assign_sampled_muts, generate_cluster_ordering, keep_temp_files,
min_frac_muts_cluster, min_muts_cluster, mut.assignment.type,
no.iters, no.iters.burn.in, num_muts_sample, species
The following objects are masked _by_ .GlobalEnv:
cellularity, datafiles, is.male, mutphasingfiles, samplename,
subsamples
The following object is masked _by_ .GlobalEnv:
seed
[1] "Loading data..."
Error in chromosome[, s] <- list_of_tables[[s]][, Chromosome] :
number of items to replace is not a multiple of replacement length
Calls: RunDP -> load.data -> load.data.inner
Execution halted
Work dir:
/scratch/e3/cf0259876c1768a25ea46be8f5c564
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
Running SomaticSniper-Battenberg-DPClust single-region mode worked fine. Same issue for Strelka2/Mutect2-Battenberg-DPClust-mr. Could this be do to the naming conventions in multi-region mode?
ERRRORING: example error log:
/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-somaticsniper-battenberg-dpclust/logs/ILHNLNEV000001_51404_SomaticSniper-Battenberg-DPClust-mr.logerror message: