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ICGC-TCGA-PanCancer / dkfz_dockered_workflows

This is the container that houses the Roddy-based component provided by DKFZ for the DEWrapper workflow
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Not compatible with test data, fails on purity-ploidy step #7

Open denis-yuen opened 8 years ago

denis-yuen commented 8 years ago 
/mnt/datastore/bundledFiles/centralBinaries/R-2.15.0/bin/Rscript --vanilla /mnt/datastore/testdata/run_id/roddyExecutionStore/exec_160908_223611160_roddy_copyNumberEstimation/analysisTools/copyNumberEstimationWorkflow/purity_ploidy_estimation_final.R --segments /mnt/datastore/testdata/run_id/ACEseq/run_id_combi_level.txt --file_sex /mnt/datastore/testdata/run_id/ACEseq/run_id_sex.txt --purity_ploidy /mnt/datastore/testdata/run_id/ACEseq/run_id_ploidy_purity_2D.txt_tmp --out /mnt/datastore/testdata/run_id/ACEseq --min_length_purity 1000000 --min_hetSNPs_purity 500 --dh_Stop max --min_length_dh_stop 1000000 --dh_zero no --purity_min 0.3 --purity_max 1.0 --ploidy_min 1.0 --ploidy_max 6.5 --pid run_id

Attaching package: 'reshape2'

The following object(s) are masked from 'package:reshape':

    colsplit, melt, recast

Loading required package: methods
segments: /mnt/datastore/testdata/run_id/ACEseq/run_id_combi_level.txt
sex: /mnt/datastore/testdata/run_id/ACEseq/run_id_sex.txt
purity_ploidy_out: /mnt/datastore/testdata/run_id/ACEseq/run_id_ploidy_purity_2D.txt_tmp
out: /mnt/datastore/testdata/run_id/ACEseq
min_length_purity: 1e+06
min_hetSNPs_purity: 500
dh_Stop: max
min_length_dh_stop: 1e+06
dh_zero: no
purity_min: 0.3
purity_max: 1
ploidy_min: 1
ploidy_max: 6.5
pid: run_id
WARNING: no segments thath fullfill requirements found, check mappability and required coverage in functions.R

Seeing the following error with the test data, input is https://github.com/ICGC-TCGA-PanCancer/dkfz_dockered_workflows/blob/develop/Dockstore.json with the bedpe file salvaged from a test run of delly

denis-yuen commented 8 years ago

In discussion with @briandoconnor this seems like a test data issue. Re-running with some real pan-cancer data to see if this is an issue with the cut-down test data.

denis-yuen commented 8 years ago

I think we're past this now, I've verified that using real data does not seem to have this issue. Changing this to a feature request since it would still be nice to have this do something reasonable for test data.