No results, no exception thrown with failed ichorCNA snakemake
MUppal opened this issue · comments
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!
