{"action":"created","issue":{"url":"https://api.github.com/repos/Illumina/canvas/issues/8","repository_url":"https://api.github.com/repos/Illumina/canvas","labels_url":"https://api.github.com/repos/Illumina/canvas/issues/8/labels{/name}","comments_url":"https://api.github.com/repos/Illumina/canvas/issues/8/comments","events_url":"https://api.github.com/repos/Illumina/canvas/issues/8/events","html_url":"https://github.com/Illumina/canvas/issues/8","id":157053319,"number":8,"title":"Error during first run","user":{"login":"lonestar21","id":9285915,"avatar_url":"https://avatars.githubusercontent.com/u/9285915?v=3","gravatar_id":"","url":"https://api.github.com/users/lonestar21","html_url":"https://github.com/lonestar21","followers_url":"https://api.github.com/users/lonestar21/followers","following_url":"https://api.github.com/users/lonestar21/following{/other_user}","gists_url":"https://api.github.com/users/lonestar21/gists{/gist_id}","starred_url":"https://api.github.com/users/lonestar21/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lonestar21/subscriptions","organizations_url":"https://api.github.com/users/lonestar21/orgs","repos_url":"https://api.github.com/users/lonestar21/repos","events_url":"https://api.github.com/users/lonestar21/events{/privacy}","received_events_url":"https://api.github.com/users/lonestar21/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":12,"created_at":"2016-05-26T18:53:42Z","updated_at":"2016-06-28T19:09:25Z","closed_at":null,"body":"Hi There,\r\nThis 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?\r\n\r\n\r\n\r\n\r\n```\r\n/opt/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 \r\n5/26/2016,10:10:39.729,Running Canvas Somatic-WGS 1.3.9.0\r\n5/26/2016,10:10:39.730,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\r\n5/26/2016,10:10:40.249,Running checkpoint 1: 'CanvasSNV'\r\n5/26/2016,10:10:40.284,Running checkpoint 2: 'CanvasBin'\r\n5/26/2016,10:10:40.640,Launch process: /opt/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\" \r\n5/26/2016,10:10:40.640,Launch process: /opt/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\" \r\n5/26/2016,10:10:40.640,Launch process: /opt/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\" \r\n5/26/2016,10:10:40.640,Launch process: /opt/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\" \r\n5/26/2016,10:10:40.640,Launch process: /opt/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\" \r\n5/26/2016,10:10:40.640,Launch process: /opt/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\" \r\n5/26/2016,10:10:40.641,Launch process: /opt/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\" \r\n5/26/2016,10:10:40.641,Launch process: /opt/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\" \r\n5/26/2016,10:19:52.911,Launch process: /opt/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\" \r\n5/26/2016,10:21:33.514,Launch process: /opt/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\" \r\n5/26/2016,10:26:48.713,Launch process: /opt/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\" \r\n5/26/2016,10:29:11.423,Launch process: /opt/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\" \r\n5/26/2016,10:31:13.998,Launch process: /opt/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\" \r\n5/26/2016,10:31:48.709,Launch process: /opt/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\" \r\n5/26/2016,10:32:00.968,Launch process: /opt/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\" \r\n5/26/2016,10:32:49.648,Launch process: /opt/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\" \r\n5/26/2016,10:33:00.067,Launch process: /opt/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\" \r\n5/26/2016,10:35:05.512,Launch process: /opt/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\" \r\n5/26/2016,10:37:33.932,Launch process: /opt/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\" \r\n5/26/2016,10:38:55.683,Launch process: /opt/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\" \r\n5/26/2016,10:39:29.808,Launch process: /opt/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\" \r\n5/26/2016,10:39:39.565,Launch process: /opt/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\" \r\n5/26/2016,10:40:31.859,Launch process: /opt/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\" \r\n5/26/2016,10:40:40.170,Launch process: /opt/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\" \r\n5/26/2016,10:43:25.457,Max job memory (GB): 2.4\r\n5/26/2016,10:43:25.457,Longest job runtime (Hours): 0.37\r\n5/26/2016,10:43:25.463,DoWorkParallelThreads, attempt 1 of 1\r\n5/26/2016,10:43:25.463,Launch process: /opt/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 \r\n5/26/2016,10:57:35.898,Max job memory (GB): 22.8\r\n5/26/2016,10:57:35.898,Longest job runtime (Hours): 0.24\r\n5/26/2016,10:57:35.899,Elapsed time (step/time(sec)/name)\t2\t00:46:55.6\tCanvasBin\r\n5/26/2016,10:57:35.899,Saving checkpoint results to /projects/rcorbettprj2/CNV_2016/Canvas/out/Checkpoints/02-CanvasBin.json\r\n5/26/2016,10:57:36.447,Running checkpoint 3: 'CanvasClean'\r\n5/26/2016,10:57:36.631,Launch process: /opt/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\"\r\n5/26/2016,10:58:34.192,Max job memory (GB): 1.9\r\n5/26/2016,10:58:34.193,Longest job runtime (Hours): 0.02\r\n5/26/2016,10:58:34.193,Elapsed time (step/time(sec)/name)\t3\t00:00:57.7\tCanvasClean\r\n5/26/2016,10:58:34.193,Saving checkpoint results to /projects/rcorbettprj2/CNV_2016/Canvas/out/Checkpoints/03-CanvasClean.json\r\n5/26/2016,10:58:34.280,Running checkpoint 4: 'CanvasPartition'\r\n5/26/2016,10:58:34.286,Launch process: /opt/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\" \r\n5/26/2016,10:59:14.586,Max job memory (GB): 1.8\r\n5/26/2016,10:59:14.586,Longest job runtime (Hours): 0.01\r\n5/26/2016,10:59:14.586,Elapsed time (step/time(sec)/name)\t4\t00:00:40.3\tCanvasPartition\r\n5/26/2016,10:59:14.586,Saving checkpoint results to /projects/rcorbettprj2/CNV_2016/Canvas/out/Checkpoints/04-CanvasPartition.json\r\n5/26/2016,10:59:14.610,ERROR: Canvas workflow error: System.InvalidOperationException: Operation is not valid due to the current state of the object\r\n  at System.IO.StreamWriter.CheckState () [0x00000] in <filename unknown>:0 \r\n  at System.IO.StreamWriter.Write (System.String value) [0x00000] in <filename unknown>:0 \r\n  at System.IO.CStreamWriter.Write (System.String val) [0x00000] in <filename unknown>:0 \r\n  at System.IO.TextWriter.Write (System.String format, System.Object arg0) [0x00000] in <filename unknown>:0 \r\n  at System.IO.TextWriter.WriteLine (System.String format, System.Object arg0) [0x00000] in <filename unknown>:0 \r\n  at System.IO.SynchronizedWriter.WriteLine (System.String format, System.Object value) [0x00000] in <filename unknown>:0 \r\n  at System.Console.WriteLine (System.String format, System.Object arg0) [0x00000] in <filename unknown>:0 \r\n  at Illumina.SecondaryAnalysis.CanvasRunner.InvokeCanvasSnv (Canvas.CanvasCallset callset) [0x00000] in <filename unknown>:0 \r\n  at Illumina.SecondaryAnalysis.CanvasRunner+<>c__DisplayClass17_0.<CallSampleInternal>b__0 () [0x00000] in <filename unknown>:0 \r\n  at Isas.Shared.Checkpointing.LegacyCheckpointRunnerAsync+<>c__DisplayClass0_0.<RunCheckpointAsync>b__0 () [0x00000] in <filename unknown>:0 \r\n  at Isas.Shared.Checkpointing.LegacyCheckpointRunner+NullSandboxedCheckpoint`2[System.String,System.String].Run (System.String input, IDirectoryLocation tempDirectory) [0x00000] in <filename unknown>:0 \r\n  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 \r\n  at Isas.Shared.Checkpointing.CheckpointRunnerAsync+<>c__DisplayClass22_1`2[System.String,System.String].<WrapWithLoadingConvention>b__2 () [0x00000] in <filename unknown>:0 \r\n  at Isas.Shared.Checkpointing.CheckpointRunnerAsync+CheckpointHelper`1[System.String].<WrapWithBenchmark>b__9_0 () [0x00000] in <filename unknown>:0 \r\n  at Isas.Shared.Checkpointing.CheckpointRunnerAsync+CheckpointHelper`1[System.String].<WrapWithSave>b__10_0 () [0x00000] in <filename unknown>:0 \r\n  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 \r\n  at Isas.Shared.Checkpointing.CheckpointRunnerAsync+<>c__DisplayClass18_0`1[System.String].<SupplyNestedCheckpoint>b__0 () [0x00000] in <filename unknown>:0 \r\n  at Isas.Shared.Checkpointing.CheckpointRunnerAsync+CheckpointHelper`1[System.String].<WrapWithStopCheckpointCheck>b__12_0 () [0x00000] in <filename unknown>:0 \r\n  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 \r\n  at System.Threading.Tasks.Task.InnerInvoke () [0x00000] in <filename unknown>:0 \r\n  at System.Threading.Tasks.Task.ThreadStart () [0x00000] in <filename unknown>:0 \r\n--- End of stack trace from previous location where exception was thrown ---\r\n  at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw () [0x00000] in <filename unknown>:0 \r\n  at System.Runtime.CompilerServices.TaskAwaiter`1[TResult].GetResult () [0x00000] in <filename unknown>:0 \r\n  at Isas.Shared.Checkpointing.LegacyCheckpointRunnerAsync+<RunCheckpointAsync>d__0.MoveNext () [0x00000] in <filename unknown>:0 \r\n--- End of stack trace from previous location where exception was thrown ---\r\n  at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw () [0x00000] in <filename unknown>:0 \r\n  at System.Runtime.CompilerServices.TaskAwaiter.GetResult () [0x00000] in <filename unknown>:0 \r\n  at Illumina.SecondaryAnalysis.CanvasRunner+<CallSampleInternal>d__17.MoveNext () [0x00000] in <filename unknown>:0 \r\n--- End of stack trace from previous location where exception was thrown ---\r\n  at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw () [0x00000] in <filename unknown>:0 \r\n  at System.Runtime.CompilerServices.TaskAwaiter.GetResult () [0x00000] in <filename unknown>:0 \r\n  at Illumina.SecondaryAnalysis.CanvasRunner.CallSample (Canvas.CanvasCallset callset) [0x00000] in <filename unknown>:0 \r\n  at Canvas.TumorNormalWgsRunner.Run (ILogger logger, ICheckpointRunnerAsync checkpointRunner, IWorkManager workManager) [0x00000] in <filename unknown>:0 \r\n  at Canvas.ModeLauncher.Launch () [0x00000] in <filename unknown>:0\r\n```"},"comment":{"url":"https://api.github.com/repos/Illumina/canvas/issues/comments/229151149","html_url":"https://github.com/Illumina/canvas/issues/8#issuecomment-229151149","issue_url":"https://api.github.com/repos/Illumina/canvas/issues/8","id":229151149,"user":{"login":"eroller","id":2440289,"avatar_url":"https://avatars.githubusercontent.com/u/2440289?v=3","gravatar_id":"","url":"https://api.github.com/users/eroller","html_url":"https://github.com/eroller","followers_url":"https://api.github.com/users/eroller/followers","following_url":"https://api.github.com/users/eroller/following{/other_user}","gists_url":"https://api.github.com/users/eroller/gists{/gist_id}","starred_url":"https://api.github.com/users/eroller/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/eroller/subscriptions","organizations_url":"https://api.github.com/users/eroller/orgs","repos_url":"https://api.github.com/users/eroller/repos","events_url":"https://api.github.com/users/eroller/events{/privacy}","received_events_url":"https://api.github.com/users/eroller/received_events","type":"User","site_admin":false},"created_at":"2016-06-28T19:09:25Z","updated_at":"2016-06-28T19:09:25Z","body":"@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."}}
{"actor":{"display_login":"eroller"}}