Closed RichardCorbett closed 8 years ago
eroller
commented
8 years ago Seems like a problem writing to console. What mono version is this? Does this same error happen every time or have you only tried this once? I suspect this may be an intermittent issue, but if it occurs during every analysis then we can investigate further.
RichardCorbett
commented
8 years ago Thanks. The folder is writable and I have about 10Tb of free space (and lots of inodes available) so i don't think it was any sort of quota error. I'll try and run again and write to a different location to see what happens.
Mono version:
/opt/mono/bin/mono --version
Mono JIT compiler version 3.2.8 (tarball Wed May 25 17:33:47 PDT 2016)
Copyright (C) 2002-2014 Novell, Inc, Xamarin Inc and Contributors. www.mono-project.com
TLS: __thread
SIGSEGV: altstack
Notifications: epoll
Architecture: amd64
Disabled: none
Misc: softdebug
LLVM: supported, not enabled.
GC: sgen
3.2.8 is a bit old, so there may be a related bug there. We have tested mono 3.10.0, mono 4.0.2 and more recently mono 4.2.3
RichardCorbett
commented
8 years ago Thanks for helping with this. I'm excited to see what sort of results I can get from canvas. I tried re-running with only changing the output folder and got the same error.
Next I'll try using mono 4.0.2 to see if that helps.
RichardCorbett
commented
8 years ago We had some trouble with 4.0.2 (missing libraries) so I'm trying 3.10.0. Fingers crossed...
RichardCorbett
commented
8 years ago Looks like we're getting the same error with 3.10.0. Do you have any other suggestions I could try?
mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/Canvas.exe Somatic-WGS -b /projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam --somatic-vcf=/projects/rcorbettprj2/CNV_2016/Canvas/passed.somatic.snvs.eff.dbSNP_v137.cosmic_v64.annotations.vcf --b-allele-vcf=/projects/rcorbettprj2/CNV_2016/Canvas/A36973_5_lanes_dupsFlagged.varFilter.PASS.vcf -o /projects/rcorbettprj2/CNV_2016/Canvas/out -r /projects/rcorbettprj2/CNV_2016/Canvas/kmer.fa -g /projects/rcorbettprj2/CNV_2016/Canvas/WholeGenomeFasta -f /projects/rcorbettprj2/CNV_2016/Canvas/filter13.bed -n coloTest
5/26/2016,15:44:42.305,Running Canvas Somatic-WGS 1.3.9.0
5/26/2016,15:44:42.310,Command-line arguments: Somatic-WGS -b /projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam --somatic-vcf=/projects/rcorbettprj2/CNV_2016/Canvas/passed.somatic.snvs.eff.dbSNP_v137.cosmic_v64.annotations.vcf --b-allele-vcf=/projects/rcorbettprj2/CNV_2016/Canvas/A36973_5_lanes_dupsFlagged.varFilter.PASS.vcf -o /projects/rcorbettprj2/CNV_2016/Canvas/out -r /projects/rcorbettprj2/CNV_2016/Canvas/kmer.fa -g /projects/rcorbettprj2/CNV_2016/Canvas/WholeGenomeFasta -f /projects/rcorbettprj2/CNV_2016/Canvas/filter13.bed -n coloTest
5/26/2016,15:44:42.821,Running checkpoint 1: 'CanvasSNV'
5/26/2016,15:44:42.835,Running checkpoint 2: 'CanvasBin'
5/26/2016,15:44:43.313,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/kmer.fa" -c 1 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_1.dat"
5/26/2016,15:44:43.314,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/kmer.fa" -c 5 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_5.dat"
5/26/2016,15:44:43.314,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/kmer.fa" -c 3 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_3.dat"
5/26/2016,15:44:43.314,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/kmer.fa" -c 2 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_2.dat"
5/26/2016,15:44:43.315,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/kmer.fa" -c 6 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_6.dat"
5/26/2016,15:44:43.315,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/kmer.fa" -c 9 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_9.dat"
5/26/2016,15:44:43.315,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/kmer.fa" -c 7 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_7.dat"
5/26/2016,15:44:43.315,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/kmer.fa" -c 11 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_11.dat"
5/26/2016,15:44:43.316,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/kmer.fa" -c 21 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_21.dat"
5/26/2016,15:44:43.316,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/kmer.fa" -c 10 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_10.dat"
5/26/2016,15:44:43.316,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/kmer.fa" -c 8 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_8.dat"
5/26/2016,15:44:43.317,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/kmer.fa" -c X -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_X.dat"
5/26/2016,15:44:43.317,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/kmer.fa" -c 4 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_4.dat"
5/26/2016,15:44:43.317,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/kmer.fa" -c 13 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_13.dat"
5/26/2016,15:44:43.318,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/kmer.fa" -c 15 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_15.dat"
5/26/2016,15:44:43.318,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/kmer.fa" -c 14 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_14.dat"
5/26/2016,15:44:43.319,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/kmer.fa" -c 12 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_12.dat"
5/26/2016,15:44:43.319,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/kmer.fa" -c 16 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_16.dat"
5/26/2016,15:44:43.319,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/kmer.fa" -c 17 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_17.dat"
5/26/2016,15:44:43.319,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/kmer.fa" -c 20 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_20.dat"
5/26/2016,15:44:43.319,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/kmer.fa" -c 18 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_18.dat"
5/26/2016,15:44:43.321,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/kmer.fa" -c Y -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_Y.dat"
5/26/2016,15:44:43.321,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/kmer.fa" -c 19 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_19.dat"
5/26/2016,15:44:43.323,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/kmer.fa" -c 22 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_22.dat"
5/26/2016,16:19:02.413,Max job memory (GB): 3.7
5/26/2016,16:19:02.413,Longest job runtime (Hours): 0.57
5/26/2016,16:19:02.416,DoWorkParallelThreads, attempt 1 of 1
5/26/2016,16:19:02.417,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/kmer.fa" -f "/projects/rcorbettprj2/CNV_2016/Canvas/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0.binned" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_1.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_2.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_3.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_4.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_5.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_6.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_7.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_X.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_8.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_9.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_10.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_11.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_12.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_13.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_14.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_15.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_16.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_17.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_18.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_20.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_Y.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_19.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_22.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_21.dat" -m GCContentWeighted
5/26/2016,16:36:15.173,Max job memory (GB): 23.4
5/26/2016,16:36:15.174,Longest job runtime (Hours): 0.29
5/26/2016,16:36:15.175,Elapsed time (step/time(sec)/name) 2 00:51:32.3 CanvasBin
5/26/2016,16:36:15.176,Saving checkpoint results to /projects/rcorbettprj2/CNV_2016/Canvas/out/Checkpoints/02-CanvasBin.json
5/26/2016,16:36:15.381,Running checkpoint 3: 'CanvasClean'
5/26/2016,16:36:15.427,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasClean.exe -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0.binned" -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest.cleaned" -g -s -r -f "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/FilterRegions.txt"
5/26/2016,16:37:46.530,Max job memory (GB): 1.9
5/26/2016,16:37:46.530,Longest job runtime (Hours): 0.03
5/26/2016,16:37:46.531,Elapsed time (step/time(sec)/name) 3 00:01:31.1 CanvasClean
5/26/2016,16:37:46.531,Saving checkpoint results to /projects/rcorbettprj2/CNV_2016/Canvas/out/Checkpoints/03-CanvasClean.json
5/26/2016,16:37:46.641,Running checkpoint 4: 'CanvasPartition'
5/26/2016,16:37:46.647,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasPartition.exe -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest.cleaned" -b "/projects/rcorbettprj2/CNV_2016/Canvas/filter13.bed" -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest.partitioned"
5/26/2016,16:38:47.918,Max job memory (GB): 2.5
5/26/2016,16:38:47.918,Longest job runtime (Hours): 0.02
5/26/2016,16:38:47.918,Elapsed time (step/time(sec)/name) 4 00:01:01.2 CanvasPartition
5/26/2016,16:38:47.919,Saving checkpoint results to /projects/rcorbettprj2/CNV_2016/Canvas/out/Checkpoints/04-CanvasPartition.json
5/26/2016,16:38:47.942,ERROR: Canvas workflow error: System.InvalidOperationException: Operation is not valid due to the current state of the object
at System.IO.StreamWriter.CheckState () [0x00000] in <filename unknown>:0
at System.IO.StreamWriter.Write (System.String value) [0x00000] in <filename unknown>:0
at System.IO.CStreamWriter.Write (System.String val) [0x00000] in <filename unknown>:0
at System.IO.TextWriter.Write (System.String format, System.Object arg0) [0x00000] in <filename unknown>:0
at System.IO.TextWriter.WriteLine (System.String format, System.Object arg0) [0x00000] in <filename unknown>:0
at System.IO.SynchronizedWriter.WriteLine (System.String format, System.Object value) [0x00000] in <filename unknown>:0
at System.Console.WriteLine (System.String format, System.Object arg0) [0x00000] in <filename unknown>:0
at Illumina.SecondaryAnalysis.CanvasRunner.InvokeCanvasSnv (Canvas.CanvasCallset callset) [0x00000] in <filename unknown>:0
at Illumina.SecondaryAnalysis.CanvasRunner+<>c__DisplayClass17_0.<CallSampleInternal>b__0 () [0x00000] in <filename unknown>:0
at Isas.Shared.Checkpointing.LegacyCheckpointRunnerAsync+<>c__DisplayClass0_0.<RunCheckpointAsync>b__0 () [0x00000] in <filename unknown>:0
at Isas.Shared.Checkpointing.LegacyCheckpointRunner+NullSandboxedCheckpoint`2[System.String,System.String].Run (System.String input, IDirectoryLocation tempDirectory) [0x00000] in <filename unknown>:0
at Isas.Shared.Checkpointing.CheckpointRunnerAsync+<>c__DisplayClass23_0`2[System.String,System.String].<RunCheckpointAsync>b__0 (ICheckpointRunnerAsync checkpointer, System.String runInput, IDirectoryLocation tempDir) [0x00000] in <filename unknown>:0
at Isas.Shared.Checkpointing.CheckpointRunnerAsync+<>c__DisplayClass22_1`2[System.String,System.String].<WrapWithLoadingConvention>b__2 () [0x00000] in <filename unknown>:0
at Isas.Shared.Checkpointing.CheckpointRunnerAsync+CheckpointHelper`1[System.String].<WrapWithBenchmark>b__9_0 () [0x00000] in <filename unknown>:0
at Isas.Shared.Checkpointing.CheckpointRunnerAsync+CheckpointHelper`1[System.String].<WrapWithSave>b__10_0 () [0x00000] in <filename unknown>:0
at Isas.Shared.Checkpointing.CheckpointRunnerAsync+<>c__DisplayClass22_0`2[System.String,System.String].<WrapWithLoadingConvention>b__0 (ICheckpointRunnerAsync runner, IDirectoryLocation tempDir) [0x00000] in <filename unknown>:0
at Isas.Shared.Checkpointing.CheckpointRunnerAsync+<>c__DisplayClass18_0`1[System.String].<SupplyNestedCheckpoint>b__0 () [0x00000] in <filename unknown>:0
at Isas.Shared.Checkpointing.CheckpointRunnerAsync+CheckpointHelper`1[System.String].<WrapWithStopCheckpointCheck>b__12_0 () [0x00000] in <filename unknown>:0
at System.Threading.Tasks.TaskActionInvoker+FuncInvoke`1[TResult].Invoke (System.Threading.Tasks.Task owner, System.Object state, System.Threading.Tasks.Task context) [0x00000] in <filename unknown>:0
at System.Threading.Tasks.Task.InnerInvoke () [0x00000] in <filename unknown>:0
at System.Threading.Tasks.Task.ThreadStart () [0x00000] in <filename unknown>:0
--- End of stack trace from previous location where exception was thrown ---
at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw () [0x00000] in <filename unknown>:0
at System.Runtime.CompilerServices.TaskAwaiter`1[TResult].GetResult () [0x00000] in <filename unknown>:0
at Isas.Shared.Checkpointing.LegacyCheckpointRunnerAsync+<RunCheckpointAsync>d__0.MoveNext () [0x00000] in <filename unknown>:0
--- End of stack trace from previous location where exception was thrown ---
at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw () [0x00000] in <filename unknown>:0
at System.Runtime.CompilerServices.TaskAwaiter.GetResult () [0x00000] in <filename unknown>:0
at Illumina.SecondaryAnalysis.CanvasRunner+<CallSampleInternal>d__17.MoveNext () [0x00000] in <filename unknown>:0
--- End of stack trace from previous location where exception was thrown ---
at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw () [0x00000] in <filename unknown>:0
at System.Runtime.CompilerServices.TaskAwaiter.GetResult () [0x00000] in <filename unknown>:0
at Illumina.SecondaryAnalysis.CanvasRunner.CallSample (Canvas.CanvasCallset callset) [0x00000] in <filename unknown>:0
at Canvas.TumorNormalWgsRunner.Run (ILogger logger, ICheckpointRunnerAsync checkpointRunner, IWorkManager workManager) [0x00000] in <filename unknown>:0
at Canvas.ModeLauncher.Launch () [0x00000] in <filename unknown>:0
Hey there, I thought i should try making the reference files from scratch to make sure things work for me (in case my GRCh37 reference differed in some way). This gave me some problems as well. It seems to choke at the beginning of chr10. Maybe there is some dependency on sort order?
mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/Tools/FlagUniqueKmers/FlagUniqueKmers.exe /genomes/9606/hg19a/bwa_ind/genome/GRCh37-lite.fa GRCh37-lite.canvas.uniqKs.fa
...
>>>1 9 137000000 dict 400000000 incomplete 1088421352
>>>1 9 138000000 dict 400000000 incomplete 1089339159
>>>1 9 139000000 dict 400000000 incomplete 1090271589
>>>1 9 140000000 dict 400000000 incomplete 1091164749
>>>1 9 141000000 dict 400000000 incomplete 1092084828
>>>1 10 0 dict 400000000 incomplete 1092202763
Unhandled Exception:
System.NullReferenceException: Object reference not set to an instance of an object
at System.Collections.Generic.InternalStringComparer.Equals (System.String x, System.String y) [0x00000] in <filename unknown>:0
at System.Collections.Generic.Dictionary`2[System.String,System.Int64].ContainsKey (System.String key) [0x00000] in <filename unknown>:0
at FlagUniqueKmers.KmerChecker.ProcessOneChromosome (GenericRead fastaEntry, Int32 chromosomeIndex) [0x00000] in <filename unknown>:0
at FlagUniqueKmers.KmerChecker.Main (System.String fastaPath, System.String outputPath) [0x00000] in <filename unknown>:0
at FlagUniqueKmers.Program.Main (System.String[] args) [0x00000] in <filename unknown>:0
[ERROR] FATAL UNHANDLED EXCEPTION: System.NullReferenceException: Object reference not set to an instance of an object
at System.Collections.Generic.InternalStringComparer.Equals (System.String x, System.String y) [0x00000] in <filename unknown>:0
at System.Collections.Generic.Dictionary`2[System.String,System.Int64].ContainsKey (System.String key) [0x00000] in <filename unknown>:0
at FlagUniqueKmers.KmerChecker.ProcessOneChromosome (GenericRead fastaEntry, Int32 chromosomeIndex) [0x00000] in <filename unknown>:0
at FlagUniqueKmers.KmerChecker.Main (System.String fastaPath, System.String outputPath) [0x00000] in <filename unknown>:0
at FlagUniqueKmers.Program.Main (System.String[] args) [0x00000] in <filename unknown>:0
Probably not the right place for this, but I also notice that when I download from here:
I can't successfully download a whole folder. I can get things if I download file by file, but I can't successfully download a folder. The error I get just tells me that the download stops after what appears to be 1 or 2 gigs of downloaded data.
RichardCorbett
commented
8 years ago Just trying to rule out causes of the problem I downloaded the example data from basespace and ran the command listed on the README file. It seems I ran in to trouble in the same place as I did using our in-house generated data.
/gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/Canvas.exe Tumor-normal-enrichment -b HiSeq_2500_RR-NRC_Exome_HCC1187_N_HCC2218-26760736/HCC2218C-28317292/HCC2218C_S1.bam --normal-bam=HiSeq_2500_RR-NRC_Exome_HCC1187_N_HCC2218-26760736/HCC2218BL-28296383/HCC2218BL_S1.bam --reference hg19/kmer.fa --manifest HiSeq_2500_RR-NRC_Exome_HCC1187_N_HCC2218-26760736/HCC1187BL-28295376/Additional_Files/NexteraRapidCapture_Exome_TargetedRegions_v1.2Used.txt -g hg19 -n HCC2218C -f hg19/filter13.bed -o HCC2218_v2 --b-allele-vcf=HiSeq_2500_RR-NRC_Exome_HCC1187_N_HCC2218-26760736/HCC2218BL-28296383/HCC2218BL_S1.vcf --custom-parameters=CanvasBin,-m=TruncatedDynamicRange
5/27/2016,13:03:10.997,Running Canvas Tumor-normal-enrichment 1.3.9.0
5/27/2016,13:03:10.999,Command-line arguments: Tumor-normal-enrichment -b HiSeq_2500_RR-NRC_Exome_HCC1187_N_HCC2218-26760736/HCC2218C-28317292/HCC2218C_S1.bam --normal-bam=HiSeq_2500_RR-NRC_Exome_HCC1187_N_HCC2218-26760736/HCC2218BL-28296383/HCC2218BL_S1.bam --reference hg19/kmer.fa --manifest HiSeq_2500_RR-NRC_Exome_HCC1187_N_HCC2218-26760736/HCC1187BL-28295376/Additional_Files/NexteraRapidCapture_Exome_TargetedRegions_v1.2Used.txt -g hg19 -n HCC2218C -f hg19/filter13.bed -o HCC2218_v2 --b-allele-vcf=HiSeq_2500_RR-NRC_Exome_HCC1187_N_HCC2218-26760736/HCC2218BL-28296383/HCC2218BL_S1.vcf --custom-parameters=CanvasBin,-m=TruncatedDynamicRange
5/27/2016,13:03:12.517,Running checkpoint 1: 'CanvasSNV'
5/27/2016,13:03:12.525,Running checkpoint 2: 'CanvasBin'
5/27/2016,13:03:13.322,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/Canvas/HiSeq_2500_RR-NRC_Exome_HCC1187_N_HCC2218-26760736/HCC2218C-28317292/HCC2218C_S1.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/hg19/kmer.fa" -c chr1 -m=TruncatedDynamicRange -t "/projects/rcorbettprj2/CNV_2016/Canvas/HCC2218_v2/TempCNV_HCC2218C/manifest.txt" -f "/projects/rcorbettprj2/CNV_2016/Canvas/hg19/filter13.bed" -d 300 -o "/projects/rcorbettprj2/CNV_2016/Canvas/HCC2218_v2/TempCNV_HCC2218C/HCC2218C_0_chr1.dat"
5/27/2016,13:03:13.322,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/Canvas/HiSeq_2500_RR-NRC_Exome_HCC1187_N_HCC2218-26760736/HCC2218C-28317292/HCC2218C_S1.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/hg19/kmer.fa" -c chrX -m=TruncatedDynamicRange -t "/projects/rcorbettprj2/CNV_2016/Canvas/HCC2218_v2/TempCNV_HCC2218C/manifest.txt" -f "/projects/rcorbettprj2/CNV_2016/Canvas/hg19/filter13.bed" -d 300 -o "/projects/rcorbettprj2/CNV_2016/Canvas/HCC2218_v2/TempCNV_HCC2218C/HCC2218C_0_chrX.dat"
5/27/2016,13:03:13.322,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/Canvas/HiSeq_2500_RR-NRC_Exome_HCC1187_N_HCC2218-26760736/HCC2218C-28317292/HCC2218C_S1.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/hg19/kmer.fa" -c chr7 -m=TruncatedDynamicRange -t "/projects/rcorbettprj2/CNV_2016/Canvas/HCC2218_v2/TempCNV_HCC2218C/manifest.txt" -f "/projects/rcorbettprj2/CNV_2016/Canvas/hg19/filter13.bed" -d 300 -o "/projects/rcorbettprj2/CNV_2016/Canvas/HCC2218_v2/TempCNV_HCC2218C/HCC2218C_0_chr7.dat"
5/27/2016,13:03:13.322,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/Canvas/HiSeq_2500_RR-NRC_Exome_HCC1187_N_HCC2218-26760736/HCC2218C-28317292/HCC2218C_S1.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/hg19/kmer.fa" -c chr2 -m=TruncatedDynamicRange -t "/projects/rcorbettprj2/CNV_2016/Canvas/HCC2218_v2/TempCNV_HCC2218C/manifest.txt" -f "/projects/rcorbettprj2/CNV_2016/Canvas/hg19/filter13.bed" -d 300 -o "/projects/rcorbettprj2/CNV_2016/Canvas/HCC2218_v2/TempCNV_HCC2218C/HCC2218C_0_chr2.dat"
.............................
5/27/2016,13:09:22.910,Max job memory (GB): 3.6
5/27/2016,13:09:22.910,Longest job runtime (Hours): 0.02
5/27/2016,13:09:22.917,DoWorkParallelThreads, attempt 1 of 1
5/27/2016,13:09:22.917,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/Canvas/HiSeq_2500_RR-NRC_Exome_HCC1187_N_HCC2218-26760736/HCC2218C-28317292/HCC2218C_S1.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/hg19/kmer.fa" -f "/projects/rcorbettprj2/CNV_2016/Canvas/hg19/filter13.bed" -d 300 -o "/projects/rcorbettprj2/CNV_2016/Canvas/HCC2218_v2/TempCNV_HCC2218C/HCC2218C_0.binned" -z "1581" -i "/projects/rcorbettprj2/CNV_2016/Canvas/HCC2218_v2/TempCNV_HCC2218C/HCC2218C_0_chr1.dat" -i 5/27/2016,13:14:48.578,Max job memory (GB): 1.9
5/27/2016,13:14:48.578,Longest job runtime (Hours): 0.00
5/27/2016,13:14:48.579,Elapsed time (step/time(sec)/name) 2 00:11:36.0 CanvasBin
5/27/2016,13:14:48.579,Saving checkpoint results to /projects/rcorbettprj2/CNV_2016/Canvas/HCC2218_v2/Checkpoints/02-CanvasBin.json
5/27/2016,13:14:48.688,Running checkpoint 3: 'CanvasClean'
5/27/2016,13:14:48.689,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasClean.exe -i "/projects/rcorbettprj2/CNV_2016/Canvas/HCC2218_v2/TempCNV_HCC2218C/HCC2218C.ratio.binned" -o "/projects/rcorbettprj2/CNV_2016/Canvas/HCC2218_v2/TempCNV_HCC2218C/HCC2218C.cleaned" -g -s -r -f "/projects/rcorbettprj2/CNV_2016/Canvas/HCC2218_v2/TempCNV_HCC2218C/FilterRegions.txt" -t "/projects/rcorbettprj2/CNV_2016/Canvas/HCC2218_v2/TempCNV_HCC2218C/manifest.txt"
5/27/2016,13:14:55.879,Max job memory (GB): 1.9
5/27/2016,13:14:55.879,Longest job runtime (Hours): 0.00
5/27/2016,13:14:55.879,Elapsed time (step/time(sec)/name) 3 00:00:07.1 CanvasClean
5/27/2016,13:14:55.879,Saving checkpoint results to /projects/rcorbettprj2/CNV_2016/Canvas/HCC2218_v2/Checkpoints/03-CanvasClean.json
5/27/2016,13:14:55.911,Running checkpoint 4: 'CanvasPartition'
5/27/2016,13:14:55.912,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas-1.3.9_x64/CanvasPartition.exe -i "/projects/rcorbettprj2/CNV_2016/Canvas/HCC2218_v2/TempCNV_HCC2218C/HCC2218C.cleaned" -b "/projects/rcorbettprj2/CNV_2016/Canvas/hg19/filter13.bed" -o "/projects/rcorbettprj2/CNV_2016/Canvas/HCC2218_v2/TempCNV_HCC2218C/HCC2218C.partitioned"
5/27/2016,13:15:01.499,Max job memory (GB): 1.9
5/27/2016,13:15:01.499,Longest job runtime (Hours): 0.00
5/27/2016,13:15:01.499,Elapsed time (step/time(sec)/name) 4 00:00:05.5 CanvasPartition
5/27/2016,13:15:01.499,Saving checkpoint results to /projects/rcorbettprj2/CNV_2016/Canvas/HCC2218_v2/Checkpoints/04-CanvasPartition.json
5/27/2016,13:15:01.501,Running checkpoint 5: 'Intersect bins with manifest'
5/27/2016,13:15:02.992,Elapsed time (step/time(sec)/name) 5 00:00:01.4 Intersect bins with manifest
5/27/2016,13:15:02.992,Saving checkpoint results to /projects/rcorbettprj2/CNV_2016/Canvas/HCC2218_v2/Checkpoints/05-Intersectbinswithmanifest.json
5/27/2016,13:15:02.994,ERROR: Canvas workflow error: System.InvalidOperationException: Operation is not valid due to the current state of the object
at System.IO.StreamWriter.CheckState () [0x00000] in <filename unknown>:0
at System.IO.StreamWriter.Write (System.String value) [0x00000] in <filename unknown>:0
at System.IO.CStreamWriter.Write (System.String val) [0x00000] in <filename unknown>:0
at System.IO.TextWriter.Write (System.String format, System.Object arg0) [0x00000] in <filename unknown>:0
at System.IO.TextWriter.WriteLine (System.String format, System.Object arg0) [0x00000] in <filename unknown>:0
at System.IO.SynchronizedWriter.WriteLine (System.String format, System.Object value) [0x00000] in <filename unknown>:0
at System.Console.WriteLine (System.String format, System.Object arg0) [0x00000] in <filename unknown>:0
at Illumina.SecondaryAnalysis.CanvasRunner.InvokeCanvasSnv (Canvas.CanvasCallset callset) [0x00000] in <filename unknown>:0
at Illumina.SecondaryAnalysis.CanvasRunner+<>c__DisplayClass17_0.<CallSampleInternal>b__0 () [0x00000] in <filename unknown>:0
at Isas.Shared.Checkpointing.LegacyCheckpointRunnerAsync+<>c__DisplayClass0_0.<RunCheckpointAsync>b__0 () [0x00000] in <filename unknown>:0
at Isas.Shared.Checkpointing.LegacyCheckpointRunner+NullSandboxedCheckpoint`2[System.String,System.String].Run (System.String input, IDirectoryLocation tempDirectory) [0x00000] in <filename unknown>:0
at Isas.Shared.Checkpointing.CheckpointRunnerAsync+<>c__DisplayClass23_0`2[System.String,System.String].<RunCheckpointAsync>b__0 (ICheckpointRunnerAsync checkpointer, System.String runInput, IDirectoryLocation tempDir) [0x00000] in <filename unknown>:0
at Isas.Shared.Checkpointing.CheckpointRunnerAsync+<>c__DisplayClass22_1`2[System.String,System.String].<WrapWithLoadingConvention>b__2 () [0x00000] in <filename unknown>:0
at Isas.Shared.Checkpointing.CheckpointRunnerAsync+CheckpointHelper`1[System.String].<WrapWithBenchmark>b__9_0 () [0x00000] in <filename unknown>:0
at Isas.Shared.Checkpointing.CheckpointRunnerAsync+CheckpointHelper`1[System.String].<WrapWithSave>b__10_0 () [0x00000] in <filename unknown>:0
at Isas.Shared.Checkpointing.CheckpointRunnerAsync+<>c__DisplayClass22_0`2[System.String,System.String].<WrapWithLoadingConvention>b__0 (ICheckpointRunnerAsync runner, IDirectoryLocation tempDir) [0x00000] in <filename unknown>:0
at Isas.Shared.Checkpointing.CheckpointRunnerAsync+<>c__DisplayClass18_0`1[System.String].<SupplyNestedCheckpoint>b__0 () [0x00000] in <filename unknown>:0
at Isas.Shared.Checkpointing.CheckpointRunnerAsync+CheckpointHelper`1[System.String].<WrapWithStopCheckpointCheck>b__12_0 () [0x00000] in <filename unknown>:0
at System.Threading.Tasks.TaskActionInvoker+FuncInvoke`1[TResult].Invoke (System.Threading.Tasks.Task owner, System.Object state, System.Threading.Tasks.Task context) [0x00000] in <filename unknown>:0
at System.Threading.Tasks.Task.InnerInvoke () [0x00000] in <filename unknown>:0
at System.Threading.Tasks.Task.ThreadStart () [0x00000] in <filename unknown>:0
--- End of stack trace from previous location where exception was thrown ---
at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw () [0x00000] in <filename unknown>:0
at System.Runtime.CompilerServices.TaskAwaiter`1[TResult].GetResult () [0x00000] in <filename unknown>:0
at Isas.Shared.Checkpointing.LegacyCheckpointRunnerAsync+<RunCheckpointAsync>d__0.MoveNext () [0x00000] in <filename unknown>:0
--- End of stack trace from previous location where exception was thrown ---
at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw () [0x00000] in <filename unknown>:0
at System.Runtime.CompilerServices.TaskAwaiter.GetResult () [0x00000] in <filename unknown>:0
at Illumina.SecondaryAnalysis.CanvasRunner+<CallSampleInternal>d__17.MoveNext () [0x00000] in <filename unknown>:0
--- End of stack trace from previous location where exception was thrown ---
at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw () [0x00000] in <filename unknown>:0
at System.Runtime.CompilerServices.TaskAwaiter.GetResult () [0x00000] in <filename unknown>:0
at Illumina.SecondaryAnalysis.CanvasRunner.CallSample (Canvas.CanvasCallset callset) [0x00000] in <filename unknown>:0
at Canvas.TumorNormalEnrichmentRunner.Run (ILogger logger, ICheckpointRunnerAsync checkpointRunner, IWorkManager workManager) [0x00000] in <filename unknown>:0
at Canvas.ModeLauncher.Launch () [0x00000] in <filename unknown>:0
Just tried your new version, but it appears I am getting similar errors as before. Do you have any suggestions?
thanks, RIchard
/gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas_1.10.0/Canvas.exe Somatic-WGS -b /projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam --somatic-vcf=/projects/rcorbettprj2/CNV_2016/Canvas/passed.somatic.snvs.eff.dbSNP_v137.cosmic_v64.annotations.vcf --b-allele-vcf=/projects/rcorbettprj2/CNV_2016/Canvas/A36973_5_lanes_dupsFlagged.varFilter.PASS.vcf -o /projects/rcorbettprj2/CNV_2016/Canvas/out -r /projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/kmer.fa -g /projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/ -f /projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed -n coloTest 6/10/2016,16:56:19.327,Running Canvas Somatic-WGS 1.10.0 6/10/2016,16:56:19.335,Command-line arguments: Somatic-WGS -b /projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam --somatic-vcf=/projects/rcorbettprj2/CNV_2016/Canvas/passed.somatic.snvs.eff.dbSNP_v137.cosmic_v64.annotations.vcf --b-allele-vcf=/projects/rcorbettprj2/CNV_2016/Canvas/A36973_5_lanes_dupsFlagged.varFilter.PASS.vcf -o /projects/rcorbettprj2/CNV_2016/Canvas/out -r /projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/kmer.fa -g /projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/ -f /projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed -n coloTest 6/10/2016,16:56:19.845,Running checkpoint 1: 'CanvasSNV' 6/10/2016,16:56:19.851,Running checkpoint 2: 'CanvasBin' 6/10/2016,16:56:20.811,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas_1.10.0/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/kmer.fa" -c 1 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_1.dat" 6/10/2016,16:56:20.813,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas_1.10.0/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/kmer.fa" -c X -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_X.dat" 6/10/2016,16:56:20.813,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas_1.10.0/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/kmer.fa" -c 4 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_4.dat" 6/10/2016,16:56:20.813,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas_1.10.0/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/kmer.fa" -c 8 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_8.dat" 6/10/2016,16:56:20.813,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas_1.10.0/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/kmer.fa" -c 6 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_6.dat" 6/10/2016,16:56:20.813,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas_1.10.0/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/kmer.fa" -c 21 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_21.dat" 6/10/2016,16:56:20.813,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas_1.10.0/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/kmer.fa" -c 3 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_3.dat" 6/10/2016,16:56:20.813,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas_1.10.0/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/kmer.fa" -c 10 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_10.dat" 6/10/2016,16:56:20.813,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas_1.10.0/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/kmer.fa" -c 14 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_14.dat" 6/10/2016,16:56:20.814,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas_1.10.0/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/kmer.fa" -c 5 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_5.dat" 6/10/2016,16:56:20.814,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas_1.10.0/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/kmer.fa" -c 7 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_7.dat" 6/10/2016,16:56:20.814,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas_1.10.0/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/kmer.fa" -c 9 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_9.dat" 6/10/2016,16:56:20.814,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas_1.10.0/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/kmer.fa" -c 2 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_2.dat" 6/10/2016,16:56:20.814,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas_1.10.0/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/kmer.fa" -c 13 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_13.dat" 6/10/2016,16:56:20.814,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas_1.10.0/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/kmer.fa" -c 12 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_12.dat" 6/10/2016,16:56:20.814,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas_1.10.0/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/kmer.fa" -c 11 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_11.dat" 6/10/2016,16:56:20.815,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas_1.10.0/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/kmer.fa" -c 18 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_18.dat" 6/10/2016,16:56:20.816,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas_1.10.0/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/kmer.fa" -c 16 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_16.dat" 6/10/2016,16:56:20.816,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas_1.10.0/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/kmer.fa" -c 17 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_17.dat" 6/10/2016,16:56:20.816,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas_1.10.0/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/kmer.fa" -c 15 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_15.dat" 6/10/2016,16:56:20.818,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas_1.10.0/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/kmer.fa" -c Y -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_Y.dat" 6/10/2016,16:56:20.819,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas_1.10.0/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/kmer.fa" -c 20 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_20.dat" 6/10/2016,16:56:20.820,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas_1.10.0/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/kmer.fa" -c 19 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_19.dat" 6/10/2016,16:56:20.822,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas_1.10.0/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/kmer.fa" -c 22 -m GCContentWeighted -f "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_22.dat" 6/10/2016,17:36:18.657,Max job memory (GB): 3.7 6/10/2016,17:36:18.657,Longest job runtime (Hours): 0.67 6/10/2016,17:36:18.659,DoWorkParallelThreads, attempt 1 of 1 6/10/2016,17:36:18.659,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas_1.10.0/CanvasBin.exe -b "/projects/rcorbettprj2/CNV_2016/HMMCopy_Titan/tumour.bam" -p -r "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/kmer.fa" -f "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed" -d 100 -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0.binned" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_1.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_2.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_3.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_4.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_5.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_6.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_7.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_X.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_8.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_9.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_10.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_11.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_12.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_13.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_14.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_15.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_16.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_17.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_18.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_20.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_Y.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_19.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_22.dat" -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0_21.dat" -m GCContentWeighted 6/10/2016,18:06:30.692,Max job memory (GB): 23.8 6/10/2016,18:06:30.692,Longest job runtime (Hours): 0.50 6/10/2016,18:06:30.694,Elapsed time (step/time(sec)/name) 2 01:10:10.8 CanvasBin 6/10/2016,18:06:30.695,Saving checkpoint results to /projects/rcorbettprj2/CNV_2016/Canvas/out/Checkpoints/02-CanvasBin.json 6/10/2016,18:06:30.814,Running checkpoint 3: 'CanvasClean' 6/10/2016,18:06:30.818,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas_1.10.0/CanvasClean.exe -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest_0.binned" -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest.cleaned" -g -s -r -f "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/FilterRegions.txt" 6/10/2016,18:08:49.329,Max job memory (GB): 1.9 6/10/2016,18:08:49.329,Longest job runtime (Hours): 0.04 6/10/2016,18:08:49.330,Elapsed time (step/time(sec)/name) 3 00:02:18.5 CanvasClean 6/10/2016,18:08:49.330,Saving checkpoint results to /projects/rcorbettprj2/CNV_2016/Canvas/out/Checkpoints/03-CanvasClean.json 6/10/2016,18:08:49.355,Running checkpoint 4: 'CanvasPartition' 6/10/2016,18:08:49.358,Launch process: /gsc/software/linux-x86_64-centos6/mono-3.10.0/mono/bin/mono /home/rcorbett/bin/canvas_1.10.0/CanvasPartition.exe -i "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest.cleaned" -b "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed" -o "/projects/rcorbettprj2/CNV_2016/Canvas/out/TempCNV_coloTest/coloTest.partitioned" 6/10/2016,18:10:34.777,Max job memory (GB): 2.5 6/10/2016,18:10:34.778,Longest job runtime (Hours): 0.03 6/10/2016,18:10:34.778,Elapsed time (step/time(sec)/name) 4 00:01:45.4 CanvasPartition 6/10/2016,18:10:34.778,Saving checkpoint results to /projects/rcorbettprj2/CNV_2016/Canvas/out/Checkpoints/04-CanvasPartition.json 6/10/2016,18:10:34.783,ERROR: Canvas workflow error: System.InvalidOperationException: Operation is not valid due to the current state of the object at System.IO.StreamWriter.CheckState () [0x00000] in <filename unknown>:0 at System.IO.StreamWriter.Write (System.String value) [0x00000] in <filename unknown>:0 at System.IO.CStreamWriter.Write (System.String val) [0x00000] in <filename unknown>:0 at System.IO.TextWriter.Write (System.String format, System.Object arg0) [0x00000] in <filename unknown>:0 at System.IO.TextWriter.WriteLine (System.String format, System.Object arg0) [0x00000] in <filename unknown>:0 at System.IO.SynchronizedWriter.WriteLine (System.String format, System.Object value) [0x00000] in <filename unknown>:0 at System.Console.WriteLine (System.String format, System.Object arg0) [0x00000] in <filename unknown>:0 at Illumina.SecondaryAnalysis.CanvasRunner.InvokeCanvasSnv (Canvas.CanvasCallset callset) [0x00000] in <filename unknown>:0 at Illumina.SecondaryAnalysis.CanvasRunner+<>c__DisplayClass17_0.<CallSampleInternal>b__0 () [0x00000] in <filename unknown>:0 at Isas.Shared.Checkpointing.LegacyCheckpointRunnerAsync+<>c__DisplayClass1_01[System.String].2[System.String,System.String].<RunCheckpointAsync>b__0 (ICheckpointRunnerAsync checkpointer, System.String runInput, IDirectoryLocation tempDir) [0x00000] in <filename unknown>:0 at Isas.Shared.Checkpointing.CheckpointRunnerAsync+<>c__DisplayClass24_12[System.String,System.String].1[System.String].<WrapWithSave>b__10_0 () [0x00000] in <filename unknown>:0 at Isas.Shared.Checkpointing.CheckpointRunnerAsync+<>c__DisplayClass24_02[System.String,System.String].1[System.String].<SupplyNestedCheckpoint>b__0 () [0x00000] in <filename unknown>:0 at Isas.Shared.Checkpointing.CheckpointRunnerAsync+CheckpointHelper1[System.String].1[TResult].Invoke (System.Threading.Tasks.Task owner, System.Object state, System.Threading.Tasks.Task context) [0x00000] in <filename unknown>:0 at System.Threading.Tasks.Task.InnerInvoke () [0x00000] in <filename unknown>:0 at System.Threading.Tasks.Task.ThreadStart () [0x00000] in <filename unknown>:0 --- End of stack trace from previous location where exception was thrown --- at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw () [0x00000] in <filename unknown>:0 at System.Runtime.CompilerServices.TaskAwaiter.GetResult () [0x00000] in <filename unknown>:0 at Illumina.SecondaryAnalysis.CanvasRunner+<CallSampleInternal>d__17.MoveNext () [0x00000] in <filename unknown>:0 --- End of stack trace from previous location where exception was thrown --- at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw () [0x00000] in <filename unknown>:0 at System.Runtime.CompilerServices.TaskAwaiter.GetResult () [0x00000] in <filename unknown>:0 at Illumina.SecondaryAnalysis.CanvasRunner.CallSample (Canvas.CanvasCallset callset) [0x00000] in <filename unknown>:0 at Canvas.TumorNormalWgsRunner.Run (ILogger logger, ICheckpointRunnerAsync checkpointRunner, IWorkManager workManager) [0x00000] in <filename unknown>:0 at Canvas.ModeLauncher.Launch () [0x00000] in <filename unknown>:0
RichardCorbett
commented
8 years ago In case anyone finds this corner of the internet in the future:
I managed to get through all of the errors listed above by using mono 4.2.3. It looks like the errors were caused by using mono 3.10.
eroller
commented
8 years ago @lonestar21 sorry I missed these recent updates. Glad you got it working. I'm curious did the problems with FlagUniqueKmers also get resolved by the mono update? Also, could you send me the link again you used to download the demo. I want to make sure downloading the entire folder works.
RichardCorbett
commented
8 years ago Hi @eroller, I can only presume the problem with FlagUniqueKmers has been resolved. I've tried re-running the command, after running all night it still processes Chr1. Previously it ran much faster and crashed within 30 minutes.
I've noticed more and more that downloading references/etc is much more stable using wget on the command line then it is when clicking through my browser. This is particularly true for amazon hosted cloud storage. I think the link I used would have been the download button on this page: https://illumina.app.box.com/v/CanvasPublic/1/5612401497
eroller
commented
8 years ago Thanks, this is useful information. It seems 4.2.3 is the recommended mono version.
mattjmeier
commented
7 years ago Hello,
I think I am having some trouble related to this thread.
I'm attempting to run FlagUniqueKmers on CentOS 6 with Mono 4.4.2, and I get the error pasted below. It took several days to get this far (I don't think system resources are the problem - the server has 512 GB RAM - but then again I'm not sure if mono limits this by default?).
I am attempting to use this with the mouse genome (mm10 build) - if anyone has successfully run FlagUniqueKmers on mm10 it would be useful to know if there is something I'm missing! Thanks
Matt
>>>1 chr1 98000000 dict 85877579 incomplete 0
>>>1 chr1 99000000 dict 86711143 incomplete 0
>>>1 chr1 100000000 dict 87588628 incomplete 0
>>>1 chr1 101000000 dict 88482674 incomplete 0
>>>1 chr1 102000000 dict 89312049 incomplete 0
>>>1 chr1 103000000 dict 90164787 incomplete 0
>>>1 chr1 104000000 dict 91021627 incomplete 0
>>>1 chr1 105000000 dict 91896175 incomplete 0
>>>1 chr1 106000000 dict 92801639 incomplete 0
>>>1 chr1 107000000 dict 93729055 incomplete 0
>>>1 chr1 108000000 dict 94568579 incomplete 0
>>>1 chr1 109000000 dict 95435501 incomplete 0
Unhandled Exception:
System.NullReferenceException: Object reference not set to an instance of an object
at System.Collections.Generic.GenericEqualityComparer`1[T].Equals (System.Collections.Generic.T x, System.Collections.Generic.T y) <0x7fab20ca6320 + 0x0004d> in <filename unknown>:0
at System.Collections.Generic.Dictionary`2[TKey,TValue].FindEntry (System.Collections.Generic.TKey key) <0x401c55d0 + 0x000f3> in <filename unknown>:0
at System.Collections.Generic.Dictionary`2[TKey,TValue].ContainsKey (System.Collections.Generic.TKey key) <0x401c5590 + 0x00019> in <filename unknown>:0
at FlagUniqueKmers.KmerChecker.ProcessOneChromosome (GenericRead fastaEntry, Int32 chromosomeIndex) <0x401c4730 + 0x00540> in <filename unknown>:0
at FlagUniqueKmers.KmerChecker.Main (System.String fastaPath, System.String outputPath) <0x40199350 + 0x0025f> in <filename unknown>:0
at FlagUniqueKmers.Program.Main (System.String[] args) <0x40197d50 + 0x000bf> in <filename unknown>:0
[ERROR] FATAL UNHANDLED EXCEPTION: System.NullReferenceException: Object reference not set to an instance of an object
at System.Collections.Generic.GenericEqualityComparer`1[T].Equals (System.Collections.Generic.T x, System.Collections.Generic.T y) <0x7fab20ca6320 + 0x0004d> in <filename unknown>:0
at System.Collections.Generic.Dictionary`2[TKey,TValue].FindEntry (System.Collections.Generic.TKey key) <0x401c55d0 + 0x000f3> in <filename unknown>:0
at System.Collections.Generic.Dictionary`2[TKey,TValue].ContainsKey (System.Collections.Generic.TKey key) <0x401c5590 + 0x00019> in <filename unknown>:0
at FlagUniqueKmers.KmerChecker.ProcessOneChromosome (GenericRead fastaEntry, Int32 chromosomeIndex) <0x401c4730 + 0x00540> in <filename unknown>:0
at FlagUniqueKmers.KmerChecker.Main (System.String fastaPath, System.String outputPath) <0x40199350 + 0x0025f> in <filename unknown>:0
at FlagUniqueKmers.Program.Main (System.String[] args) <0x40197d50 + 0x000bf> in <filename unknown>:0@mattjmeier I think you are running into this issue: https://github.com/Illumina/canvas/issues/11 The workaround is to run on a windows machine. We haven't had a chance to look into the issue related to running on mono.
mattjmeier
commented
7 years ago Thanks for the response, I am trying to do this now.
It would be nice to have this run on linux because that is where our system resources are better. I'm going to try to get a Windows licence for our server and run in it in a VM, because the only Windows workstation I can use has only 16 GB RAM (which seems to get used up very quickly, and then the program starts to swap - I assume it will take forever to run this way).
It would be even better if someone who has the resources could provide references for the common model organisms -- I'm sure a lot of people would like to use Canvas "out of the box" with mm9 or mm10.
Cheers, Matt
Hi There, This is my first attempt at running this. One thing I didn't see in your docs was that I had to add the path to mono to my PATH before running. However, even after that I'm still running into an error that I can't quite understand. Does the following trace give you any ideas about what I might be doing wrong?