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Canvas - Copy number variant (CNV) calling from DNA sequencing data
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System.Collections.Generic.KeyNotFoundException: The given key '*.bam' was not present in the dictionary. #109

Open huangl07 opened 5 years ago

huangl07 commented 5 years ago

dear canvas support

I have run a canvas worksh like dotnet $prefix/Canvas-1.39.0.1598+master_x64/Canvas.dll Germline-WGS --bam=FAM1201802.mkdup.bam --sample-b-allele-vcf=out.recode.vcf -r Genome/ref_1/ref/ref/Sequence/WholeGenomeFASTA/genome.fa -g Genome/ -o FAM1201802-cnv --sample-name=FAM1201802 --filter-bed=1.bed

but it turns out 2018-12-12T10:53:03+08:00, 2018-12-12T10:53:03+08:00,Running checkpoint 01: Validate input 2018-12-12T10:53:04+08:00,Running Canvas Germline-WGS 1.39.0.1598+master 2018-12-12T10:53:04+08:00,Command-line arguments: Germline-WGS --bam=FAM1201802.mkdup.bam --sample-b-allele-vcf=out.recode.vcf -r Genome/ref_1/ref/ref/Sequence/WholeGenomeFASTA/genome.fa -g Genome/ -o FAM1201802-cnv --sample-name=FAM1201802 --filter-bed=1.bed 2018-12-12T10:53:04+08:00,Checkpoint 01 Validate input complete. Elapsed time (hh/mm/ss): 00:00:00.3 2018-12-12T10:53:05+08:00,Normal Vcf path: /mnt/ilustre/centos7users/dna/canvas/out.recode.vcf 2018-12-12T10:53:05+08:00, 2018-12-12T10:53:05+08:00,Running checkpoint 02: CanvasSNV 2018-12-12T10:53:05+08:00, 2018-12-12T10:53:05+08:00,Running checkpoint 03: CanvasBin Invoking 0 processor jobs...for sample FAM1201802 CanvasSNV start for sample FAM1201802 CanvasSNV complete for sample FAM1201802 2018-12-12T10:53:05+08:00,Begin converting '/mnt/ilustre/centos7users/dna/canvas/FAM1201802-cnv/TempCNV_FAM1201802/VFResultsFAM1201802.txt.gz.baf' to '/mnt/ilustre/centos7users/dna/canvas/FAM1201802-cnv/TempCNV_FAM1201802/ballele.bedgraph.gz' 2018-12-12T10:53:05+08:00,ERROR: Canvas workflow error: System.Collections.Generic.KeyNotFoundException: The given key '/mnt/ilustre/centos7users/dna/canvas/FAM1201802.mkdup.bam' was not present in the dictionary. at System.Collections.Generic.Dictionary2.get_Item(TKey key) at Canvas.CanvasRunner.<>c__DisplayClass23_0.<BamToBinned>b__0(Int32 bamIdx, WorkResources resources, IJobLauncher jobLauncher) at Isas.Framework.WorkManagement.ResourceManagement.ThreadedWorkResourceManager.<>c__DisplayClass11_01.b3(WorkResources resources) --- End of stack trace from previous location where exception was thrown --- at Isas.Framework.WorkManagement.ResourceManagement.ThreadedWorkResourceManager.b11_1[T](Task1 resourceRequestTask, Task1 functionTask) at Isas.Framework.WorkManagement.AsTaskExtensions.Await[T](Task1 task) at System.Linq.Enumerable.SelectListIterator2.ToList() at Canvas.CanvasRunner.BamToBinned(IDirectoryLocation tempFolder, Boolean isPairedEnd, List1 sampleIds, String canvasReferencePath, String canvasBedPath, List1 bamPaths, Int32 binSize, Dictionary2 intermediateDataPathsByBam) at Canvas.CanvasRunner.InvokeCanvasBin35Mers(CanvasCallset callset, String canvasReferencePath, String canvasBedPath, String ploidyVcfPath) at Canvas.CanvasRunner.InvokeCanvasBin(CanvasCallset callset, String canvasReferencePath, String canvasBedPath, String ploidyVcfPath) at Isas.Framework.Checkpointing.Internals.SerializingCheckpointRunner.<>c__DisplayClass8_01.b__0(Checkpoint checkpoint) at Isas.Framework.Checkpointing.Internals.CoreCheckpointRunner.RunCheckpoint[TResult](String name, Func`2 run) at Canvas.CanvasRunner.CallSampleInternal(CanvasCallset callset) at Canvas.CanvasRunner.CallSample(CanvasCallset callset) at Canvas.ModeLauncher.Launch() 2018-12-12T10:53:05+08:00,Launching process for job tabix-index-tmp-ballele.bedgraph.gz.1: bash -o pipefail -c " /mnt/ilustre/centos7users/dna/.env/Canvas-1.39.0.1598+master_x64/tabix -p bed -f /mnt/ilustre/centos7users/dna/canvas/FAM1201802-cnv/TempCNV_FAM1201802/ballele.bedgraph.gz " 2018-12-12T10:53:06+08:00,Job tabix-index-tmp-ballele.bedgraph.gz.1 duration: 00:00:00.0 2018-12-12T10:53:06+08:00,Finished converting '/mnt/ilustre/centos7users/dna/canvas/FAM1201802-cnv/TempCNV_FAM1201802/VFResultsFAM1201802.txt.gz.baf' to '/mnt/ilustre/centos7users/dna/canvas/FAM1201802-cnv/TempCNV_FAM1201802/ballele.bedgraph.gz'. Elapsed time: 00:00:00.1 2018-12-12T10:53:06+08:00,Checkpoint 02 CanvasSNV complete. Elapsed time (hh/mm/ss): 00:00:00.4

I check the /mnt/ilustre/centos7users/dna/canvas/FAM1201802-cnv/TempCNV_FAM1201802/VFResultsFAM1201802.txt.gz file ,it's empty

but my vcf is #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT FAM1201802 sca1 161 sca1_161 C T 333.75 PASS . GT:AD:DP:GQ:PGT:PID:PL 1/1:0,2:2:6:1|1:161_C_T:90,6,0 sca1 168 sca1_168 T A 333.75 PASS . GT:AD:DP:GQ:PGT:PID:PL 1/1:0,2:2:6:1|1:161_C_T:90,6,0 sca1 170 sca1_170 A G 333.75 PASS . GT:AD:DP:GQ:PGT:PID:PL 1/1:0,2:2:6:1|1:161_C_T:90,6,0 sca1 176 sca1_176 G A 243.87 PASS . GT:AD:DP:GQ:PGT:PID:PL 1/1:0,2:2:6:1|1:161_C_T:90,6,0 sca1 195 sca1_195 A T 199.02 PASS . GT:AD:DP:GQ:PGT:PID:PL 1/1:0,2:2:6:1|1:195_A_T:90,6,0 sca1 198 sca1_198 A G 199.02 PASS . GT:AD:DP:GQ:PGT:PID:PL 1/1:0,2:2:6:1|1:195_A_T:90,6,0 sca1 489 sca1_489 T A 918.21 PASS . GT:AD:DP:GQ:PGT:PID:PL 1/1:0,7:7:21:1|1:472_TTCGATCATATAA_T:315,21,0 sca1 491 sca1_491 C T 918.21 PASS . GT:AD:DP:GQ:PGT:PID:PL 1/1:0,7:7:21:1|1:472_TTCGATCATATAA_T:315,21,0 sca1 540 sca1_540 G A 1176.2 PASS . GT:AD:DP:GQ:PGT:PID:PL 1/1:0,11:11:36:1|1:540_G_A:534,36,0

How could I do?

thankyou!

eroller commented 5 years ago

try SmallPedigree-WGS mode, Germline-WGS has been deprecated.

huangl07 commented 5 years ago

thank you for replay me so soon，but I got the same error

$dotnet $prefix/Canvas-1.39.0.1598+master_x64/Canvas.dll SmallPedigree-WGS --bam=FAM1201802.mkdup.bam --sample-b-allele-vcf=out.recode.vcf -r Genome/ref_1/ref/ref/Sequence/WholeGenomeFASTA/genome.fa -g Genome/ -o ref.cnv.vcf -f=1.bed 2018-12-13T08:21:44+08:00, 2018-12-13T08:21:44+08:00,Running checkpoint 01: Validate input 2018-12-13T08:21:44+08:00,Running Canvas SmallPedigree-WGS 1.39.0.1598+master 2018-12-13T08:21:44+08:00,Command-line arguments: SmallPedigree-WGS --bam=FAM1201802.mkdup.bam --sample-b-allele-vcf=out.recode.vcf -r Genome/ref_1/ref/ref/Sequence/WholeGenomeFASTA/genome.fa -g Genome/ -o ref.cnv.vcf -f=1.bed 2018-12-13T08:21:45+08:00, 2018-12-13T08:21:45+08:00,Running checkpoint 02: CanvasSNV 2018-12-13T08:21:45+08:00, 2018-12-13T08:21:45+08:00,Running checkpoint 03: CanvasBin 2018-12-13T08:21:46+08:00,ERROR: Canvas workflow error: System.Collections.Generic.KeyNotFoundException: The given key '/mnt/ilustre/users/long.huang/newmdt/WTH/Var/04.bam-mkdup/c1-1.mkdup.bam' was not present in the dictionary. at System.Collections.Generic.Dictionary2.get_Item(TKey key) at Canvas.CanvasRunner.<>c__DisplayClass23_0.<BamToBinned>b__0(Int32 bamIdx, WorkResources resources, IJobLauncher jobLauncher) at Isas.Framework.WorkManagement.ResourceManagement.ThreadedWorkResourceManager.<>c__DisplayClass11_01.b3(WorkResources resources) --- End of stack trace from previous location where exception was thrown --- at Isas.Framework.WorkManagement.ResourceManagement.ThreadedWorkResourceManager.b11_1[T](Task1 resourceRequestTask, Task1 functionTask) at Isas.Framework.WorkManagement.AsTaskExtensions.Await[T](Task1 task) at System.Linq.Enumerable.SelectListIterator2.ToList() at Canvas.CanvasRunner.BamToBinned(IDirectoryLocation tempFolder, Boolean isPairedEnd, List1 sampleIds, String canvasReferencePath, String canvasBedPath, List1 bamPaths, Int32 binSize, Dictionary2 intermediateDataPathsByBam) at Canvas.CanvasRunner.InvokeCanvasBin(SmallPedigreeCallset callset, String canvasReferencePath, String canvasBedPath) at Isas.Framework.Checkpointing.Internals.SerializingCheckpointRunner.<>c__DisplayClass8_01.b__0(Checkpoint checkpoint) at Isas.Framework.Checkpointing.Internals.CoreCheckpointRunner.RunCheckpoint[TResult](String name, Func`2 run) at Canvas.CanvasRunner.CallSampleInternal(SmallPedigreeCallset callset) at Canvas.CanvasRunner.CallPedigree(SmallPedigreeCallset callset) at Canvas.ModeLauncher.Launch()

thankyou！

eroller commented 5 years ago

try using an absolute path to the bam rather than a relative path

huangl07 commented 5 years ago

sorry bother that I have already use absolute path ，but the result is same