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gavinha / TitanCNA

Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
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No results, no exception thrown with failed ichorCNA snakemake #59

Closed MUppal closed 5 years ago

MUppal commented 5 years ago

Hi, I'm having trouble having the snakemake output results. I'm attempting to run the command "snakemake -s ichorCNA.snakefile -np" and get the following output (see below). I unfortunately can't tell clearly the error from the output, as the output does not explicitly throw an exception or state which process/dependency might be improperly linked to in config.yaml. It would seem that the output of the command would be in the "results" directory, but there is none to be found.

I'm using the following versions of software: TitanCNA - 1.17.0 (I believe the current version in the Titan snakemake repo) ichorCNA - 0.1.0 HMMcopy - 1.24.0 optparse - 1.6.0 SNPchip - 2.28.0 stringr - 1.3.1

Python-3.5.2 snakemake - 3.12.0 PySAM-0.15.1 PyYAML-3.13

samtools-1.3.1 HMM_Copy_Utils-1.0

rule read_counter: input: /home/ubuntu/Sample_PM1043_Z11_1_p2_Case_HALO.md.bam output: results/readDepth/tumor_sample_1.bin10000.wig log: logs/readDepth/tumor_sample_1.bin10000.log jobid: 1 wildcards: samples=tumor_sample_1, binSize=10000 resources: mem=4

/home/ubuntu/hmmcopy_utils/bin/readCounter /home/ubuntu/Sample_PM1043_Z11_1_p2_Case_HALO.md.bam -c 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y -w 10000 -q 20 > results/readDepth/tumor_sample_1.bin10000.wig 2> logs/readDepth/tumor_sample_1.bin10000.log

rule read_counter: input: /home/ubuntu/Sample_PM1043_EBC4_2_p2_Ctrl_HALO.md.bam output: results/readDepth/normal_sample_1.bin10000.wig log: logs/readDepth/normal_sample_1.bin10000.log jobid: 3 wildcards: samples=normal_sample_1, binSize=10000 resources: mem=4

/home/ubuntu/hmmcopy_utils/bin/readCounter /home/ubuntu/Sample_PM1043_EBC4_2_p2_Ctrl_HALO.md.bam -c 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y -w 10000 -q 20 > results/readDepth/normal_sample_1.bin10000.wig 2> logs/readDepth/normal_sample_1.bin10000.log

rule ichorCNA: input: results/readDepth/tumor_sample_1.bin10000.wig, results/readDepth/normal_sample_1.bin10000.wig output: results/ichorCNA/tumor_sample_1/tumor_sample_1.correctedDepth.txt, results/ichorCNA/tumor_sample_1/, results/ichorCNA/tumor_sample_1/tumor_sample_1.cna.seg log: logs/ichorCNA/tumor_sample_1.log jobid: 2 wildcards: tumor=tumor_sample_1 resources: mem=4

Rscript /home/ubuntu/ichorCNA/scripts/runIchorCNA.R --libdir /home/ubuntu/ichorCNA/R/ --id tumor_sample_1 --WIG results/readDepth/tumor_sample_1.bin10000.wig --gcWig /home/ubuntu/ichorCNA/inst/extdata/gc_hg19_10kb.wig --mapWig /home/ubuntu/ichorCNA/inst/extdata/map_hg19_10kb.wig --NORMWIG results/readDepth/normal_sample_1.bin10000.wig --ploidy "c(2,3)" --normal "c(0.5)" --maxCN 8 --includeHOMD False --genomeStyle NCBI --chrs "c(1:22, \"X\")" --estimateNormal True --estimatePloidy True --estimateScPrevalence True --scStates "c(1,3)" --centromere /home/ubuntu/ichorCNA/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt --exons.bed None --txnE 0.9999 --txnStrength 10000 --fracReadsInChrYForMale 0.001 --plotFileType png --plotYLim "c(-2,4)" --outDir results/ichorCNA/tumor_sample_1/ > logs/ichorCNA/tumor_sample_1.log 2> logs/ichorCNA/tumor_sample_1.log

localrule correctDepth: input: results/ichorCNA/tumor_sample_1/tumor_sample_1.cna.seg, results/ichorCNA/tumor_sample_1/tumor_sample_1.correctedDepth.txt, results/readDepth/tumor_sample_1.bin10000.wig, results/readDepth/normal_sample_1.bin10000.wig jobid: 0

Job counts: count jobs 1 correctDepth 1 ichorCNA 2 read_counter 4

Any help would be appreciated! Thank you!

gavinha commented 5 years ago

Hi @MUppal

For snakemake, if you use -np, it does not actually run the pipeline, but rather just displays information. For more information on snakemake, you can check out their documentation.

Best, Gavin