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How do I get the Canvas reference data for, say, GRCh37? I looked at https://illumina.box.com/CanvasPublic but that link appears to be dead, or there is nothing in there. Does anyone know the current location for the Canvas reference data?

Thanks,
Susan.

I attempted to download the hg38 and GRCh37 reference genome files, but the link isn't working. When I click it, I get the following error message:

This shared file or folder link has been removed or is unavailable to you.

Also, I would like to build these files for additional reference genomes, but I cannot find any use instructions for how to do this using the FlagUniqueKmers file.

Thanks in advance for your help.

Justin

Dear developer,
I'm interested in using Canvas for CNV calling of a germline sample from targeted sequencing data (gene panel), but having a look at the available modes, there isn't a mode for my experiment. Not sure if I can use Germline-WGS instead...
Thanks!
Javier

Hi,

I am running Canvas on tumor WGS samples and get the following error. I have attached the stderr file, please let me know what other information you might need.
SomaticCNV.stderr.txt
This error has occurred only on some samples that I have been testing.

Thanks,
Minita

Hello,

I'm trying to test Canvas on a human sample and it's giving me errors. It says:

Canvas workflow error: Isas.Shared.JobFailedException: mono returned error code 1

I also attached the CanvasError.txt that is produced. Would appreciate your help.
CanvasLog.txt

Is it possible to use Canvas to call CNV without a matched-normal bam file? I.e. I have targeted sequence data from tumors from multiple subjects, and targeted sequence from normal tissue for a subset of those. Is it possible to use Canvas to call CNV alterations on the unmatched tumor data? If so, how? Can I just dump in an unmatched normal BAM in the --normal-bam=... as follows?

mono Canvas.exeTumor-normal-enrichment -b subject1-tumor.bam --normal-bam=subject1-normal.bam

Hi,
I am trying to use the Canvas tool for WGS CNV detection.

Instructions says we can download the hg19 reference fasta (and I hope xml file) using the https://illumina.box.com/CanvasPublic link, but is looks like files have been moved.

I also tried to make the reference files using the command:
dotnet ~/canvas-1.25.0/Tools/FlagUniqueKmers/FlagUniqueKmers.dll ~/refs/M_hg19_ucsc_all.fa ~/M_hg19_ucsc_all.Canvas.fa

But it failed with error "Unhandled Exception: OutOfMemoryException."

I am running over 128GB RAM ubuntu server.

Any recommendation will be helpful.

Amit

Hello,

My name is Rabia and I am trying to run the demo for Canvas with the provided data sets/files but seem to be running into errors. I used the exact commands and files as specified in both the Canvas documentation: https://github.com/Illumina/canvas/blob/master/SoftwareDesignDocument.pdf and readme at github: https://github.com/Illumina/canvas, and got the same error both times. I would appreciate any help into resolving this issue and so that I am sure that canvas is successfully installed and running on my computer(linux).

Thank you,
CanvasError.txt

Rabia

My terminal command:

/home/rabia/Desktop/Canvas_Test# /usr/bin/mono /home/rabia/Programs/Canvas/Canvas.exe Tumor-normal-enrichment -b HCC1187C_S1.bam --normal-bam=HCC1187BL_S1.bam --reference=kmer.fa --manifest=nexterarapidcapture_expandedexome_targetedregions.txt -g hg19_genome/ -n HCC1187 -f filter13.bed -o out --b-allele-vcf=dbsnp.vcf --custom-parameters=CanvasBin,-m=TruncatedDynamicRange

Error log:
11/16/2016,15:00:23.003,ERROR: Canvas workflow error: System.TypeInitializationException: The type initializer for 'Newtonsoft.Json.JsonWriter' threw an exception. ---> System.BadImageFormatException: Could not resolve field token 0x04000493
File name: 'Newtonsoft.Json'
at Newtonsoft.Json.JsonWriter.BuildStateArray () <0x417b26c0 + 0x0008b> in :0
at Newtonsoft.Json.JsonWriter..cctor () <0x417b22c0 + 0x003cf> in :0
--- End of inner exception stack trace ---
at Newtonsoft.Json.JsonTextWriter..ctor (System.IO.TextWriter textWriter) <0x417b2190 + 0x00017> in :0
at Newtonsoft.Json.JsonConvert.SerializeObjectInternal (System.Object value, System.Type type, Newtonsoft.Json.JsonSerializer jsonSerializer) <0x417b1f70 + 0x000c3> in :0
at Newtonsoft.Json.JsonConvert.SerializeObject (System.Object value, System.Type type, Formatting formatting, Newtonsoft.Json.JsonSerializerSettings settings) <0x417b0630 + 0x0004b> in :0
at Newtonsoft.Json.JsonConvert.SerializeObject (System.Object value, Formatting formatting, Newtonsoft.Json.JsonSerializerSettings settings) <0x417b0540 + 0x00023> in :0
at Isas.Shared.Checkpointing.CheckpointJsonSerializerAsync.Serialize[T] (IFileLocation path, Isas.Shared.Checkpointing.T obj) <0x417b0120 + 0x000a7> in :0
at Isas.Shared.Checkpointing.CheckpointJsonSerializerAsync.Save[T] (Isas.Shared.Checkpointing.Checkpoint checkpoint, Isas.Shared.Checkpointing.T output) <0x417b0030 + 0x000a7> in :0
at Isas.Shared.Checkpointing.CheckpointRunnerAsync+CheckpointHelper1[T].<WrapWithSave>b__10_0 () <0x41753680 + 0x00082> in <filename unknown>:0 at Isas.Shared.Checkpointing.CheckpointRunnerAsync+CheckpointHelper1[T].b__12_0 () <0x41750410 + 0x0001e> in :0
at System.Threading.Tasks.Task1[TResult].InnerInvoke () <0x7f9e0508cb10 + 0x00053> in <filename unknown>:0 at System.Threading.Tasks.Task.Execute () <0x7f9e0509e050 + 0x00055> in <filename unknown>:0 --- End of stack trace from previous location where exception was thrown --- at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw () <0x7f9e050016d0 + 0x00029> in <filename unknown>:0 at System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess (System.Threading.Tasks.Task task) <0x7f9e04fff6b0 + 0x000a7> in <filename unknown>:0 at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification (System.Threading.Tasks.Task task) <0x7f9e04fff630 + 0x0006b> in <filename unknown>:0 at System.Runtime.CompilerServices.TaskAwaiter.ValidateEnd (System.Threading.Tasks.Task task) <0x7f9e04fff5e0 + 0x0003a> in <filename unknown>:0 at System.Runtime.CompilerServices.TaskAwaiter1[TResult].GetResult () <0x7f9e04fff8d0 + 0x00017> in :0
at Isas.Shared.Checkpointing.CheckpointRunnerAsync.RunCheckpoint[TOut] (System.String key, System.Func`1 function) <0x41750320 + 0x000ac> in :0
at Illumina.SecondaryAnalysis.CanvasRunner+d__17.MoveNext () <0x4174dd90 + 0x00549> in :0
--- End of stack trace from previous location where exception was thrown ---
at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw () <0x7f9e050016d0 + 0x00029> in :0
at System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess (System.Threading.Tasks.Task task) <0x7f9e04fff6b0 + 0x000a7> in :0
at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification (System.Threading.Tasks.Task task) <0x7f9e04fff630 + 0x0006b> in :0
at System.Runtime.CompilerServices.TaskAwaiter.ValidateEnd (System.Threading.Tasks.Task task) <0x7f9e04fff5e0 + 0x0003a> in :0
at System.Runtime.CompilerServices.TaskAwaiter.GetResult () <0x7f9e04fff5c0 + 0x00012> in :0
at Illumina.SecondaryAnalysis.CanvasRunner.CallSample (Canvas.CanvasCallset callset) <0x4174d4a0 + 0x001b3> in :0
at Canvas.TumorNormalEnrichmentRunner.Run (ILogger logger, ICheckpointRunnerAsync checkpointRunner, IWorkManager workManager) <0x41747220 + 0x0009b> in :0
at Canvas.ModeLauncher.Launch () <0x4170dcc0 + 0x002a6> in :0

Hi,

Is it possible to alter the 100kb binning sizes in the CNV.CoverageAndVariantFrequency.txt file? I've been looking around but can't seem to find an option for it...

Regards
Per Sikora

Getting the error below running Canvas Somatic-Enrichment.
The thing is that the files are actually there. If I go on to run CanvasPartition etc manually then it all works.

18/08/2016,11:03:16.264,Launch process: C:\1.11.0\CanvasClean.exe -i "C:\Canvas_test\TempCNV_sample1\sample1_0.binned"
-o "C:\Canvas_test\TempCNV_sample1\sample1.cleaned" -g -t "C:\Canvas_test\TempCNV_sample1\manifest.txt"
18/08/2016,11:03:16.997,Max job memory (GB): 0.0
18/08/2016,11:03:16.997,Longest job runtime (Hours): 0.00
18/08/2016,11:03:17.200,ERROR: Canvas workflow error: System.ArgumentNullException: Value cannot be null.
Parameter name: fileName
at System.IO.FileInfo..ctor(String fileName)
at Illumina.SecondaryAnalysis.CanvasRunner.InvokeCanvasClean(CanvasCallset callset, IFileLocation binnedPath) in D:\T
eamCity\buildAgent\work\7ce21c24b500a92f\Src\Canvas\Canvas\CanvasRunner.cs:line 637
at Isas.Shared.Checkpointing.CheckpointRunnerAsync.CheckpointHelper1.<WrapWithBenchmark>b__9_0() at Isas.Shared.Checkpointing.CheckpointRunnerAsync.CheckpointHelper1.b__10_0()
at Isas.Shared.Checkpointing.CheckpointRunnerAsync.CheckpointHelper1.<WrapWithStopCheckpointCheck>b__12_0() at System.Threading.Tasks.Task1.InnerInvoke()
at System.Threading.Tasks.Task.Execute()
--- End of stack trace from previous location where exception was thrown ---
at System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(Task task)
at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(Task task)
at Isas.Shared.Checkpointing.CheckpointRunnerAsync.RunCheckpoint[TOut](String key, Func`1 function)
at Illumina.SecondaryAnalysis.CanvasRunner.d__17.MoveNext() in D:\TeamCity\buildAgent\work\7ce21c
24b500a92f\Src\Canvas\Canvas\CanvasRunner.cs:line 532
--- End of stack trace from previous location where exception was thrown ---
at System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(Task task)
at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(Task task)
at Illumina.SecondaryAnalysis.CanvasRunner.CallSample(CanvasCallset callset) in D:\TeamCity\buildAgent\work\7ce21c24b
500a92f\Src\Canvas\Canvas\CanvasRunner.cs:line 498
at Canvas.ModeLauncher.Launch() in D:\TeamCity\buildAgent\work\7ce21c24b500a92f\Src\Canvas\Canvas\ModeLauncher.cs:lin
e 61

Thanks.

Cheers,
Peter

Hello,

I am confused about which parameters should be set for an FFPE tumour run without a matched normal.
My specific questions are:

1. Is the Somatic-Enrichment workflow correct for targeted sequencing on an unmatched FFPE tumour?
2. Is it wise to use a non-FFPE unmatched normal control sample with an FFPE tumour? I recall you saying this was not helpful, so I have not defined a control sample below.
3. When specifying custom parameters to multiple tools, is each tool specification separated by a semicolon?
4. Are the custom parameters below appropriate for an FFPE sample?
5. Which custom parameters are set for each step of the Somatic-Enrichment workflow by default?

At the moment what I have is the following (values inside <> are my files):

Canvas.exe Somatic-Enrichment --bam=<TUMOUR_FFPE.BAM>
--manifest=
--b-allele-vcf=dbsnp.vcf
--exclude-non-het-b-allele-sites=TRUE
--output=<OUT_DIR> --reference=kmer.fa
--genome-folder=<GENOME_DIR>
--sample_name=
--custom-parameters=CanvasBin,-m=TruncatedDynamicRange;CanvasClean,--ffpeoutliers=TRUE

Thank you very much for your time, sorry for the many questions.

Cheers,
Peter

ADDIT: I just saw in the source code of CanvasClean.exe that ffpeoutliers is not recommended for targeted data - so for Somatic-Enrichment it should be turned off?

Hi there,
I'm trying to run a set of analyses to see what sort of results I get for various tumours. On my seventh tumour-normal pair, I got this error. If I start from scratch and try again I get the same error.

 /gsc/software/linux-x86_64-centos6/mono-4.2.3/bin/mono /home/rcorbett/bin/1.11.0/CanvasSomaticCaller.exe -v /projects/rcorbettprj2/CNV_2016/tests/POG558/out/TempCNV_POG558/VFResultsPOG558.txt.gz -i /projects/rcorbettprj2/CNV_2016/tests/POG558/out/TempCNV_POG558/POG558.partitioned -o /projects/rcorbettprj2/CNV_2016/tests/POG558/out/CNV.vcf.gz -b /projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed -n POG558 -f "/projects/rcorbettprj2/CNV_2016/tests/POG558/out/TempCNV_POG558/FilterRegions.txt" -s /projects/rcorbettprj2/CNV_2016/tests/POG558/passed.somatic.snvs.eff.vcf -r "/projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/"
>>>Command-line arguments:
-v /projects/rcorbettprj2/CNV_2016/tests/POG558/out/TempCNV_POG558/VFResultsPOG558.txt.gz -i /projects/rcorbettprj2/CNV_2016/tests/POG558/out/TempCNV_POG558/POG558.partitioned -o /projects/rcorbettprj2/CNV_2016/tests/POG558/out/CNV.vcf.gz -b /projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/filter13.bed -n POG558 -f /projects/rcorbettprj2/CNV_2016/tests/POG558/out/TempCNV_POG558/FilterRegions.txt -s /projects/rcorbettprj2/CNV_2016/tests/POG558/passed.somatic.snvs.eff.vcf -r /projects/rcorbettprj2/CNV_2016/Canvas/GRCh37/ 
>>> Loaded 416 intervals for 24 sequences
7/8/2016 8:20:26 AM CallVariants start:
7/8/2016 8:20:26 AM Read segments from /projects/rcorbettprj2/CNV_2016/tests/POG558/out/TempCNV_POG558/POG558.partitioned
7/8/2016 8:20:37 AM Loaded 4268 segments
7/8/2016 8:20:37 AM Load variant frequencies from /projects/rcorbettprj2/CNV_2016/tests/POG558/out/TempCNV_POG558/VFResultsPOG558.txt.gz
7/8/2016 8:20:40 AM Loaded a total of 2277581 usable variant frequencies
7/8/2016 8:20:40 AM Initialize ploidy models...
7/8/2016 8:20:40 AM Ploidy models prepared.
Modeling overall coverage/purity across 3293 segments
>>> Running density clustering for cutoff 0.06000 , number of clusters 4
>>> Running density clustering for cutoff 0.05480 , number of clusters 4
>>> Running density clustering for cutoff 0.04960 , number of clusters 5
>>> Running density clustering for cutoff 0.04440 , number of clusters 5
>>> Running density clustering for cutoff 0.03920 , number of clusters 7
>>> Running density clustering for cutoff 0.03400 , number of clusters 7
>>> Running density clustering for cutoff 0.02880 , number of clusters 11
>>> Running density clustering for cutoff 0.02360 , number of clusters 11
>>> Running density clustering for cutoff 0.01840 , number of clusters 13
>>> Running density clustering for cutoff 0.01320 , number of clusters 13
>>> Running density clustering for cutoff 0.00800 , number of clusters 17

Unhandled Exception:
System.ArgumentOutOfRangeException: Index was out of range. Must be non-negative and less than the size of the collection.
Parameter name: index
  at System.ThrowHelper.ThrowArgumentOutOfRangeException () <0x7fa81a500d10 + 0x00034> in <filename unknown>:0 
  at System.Collections.Generic.List`1[T].get_Item (Int32 index) <0x7fa81a723ed0 + 0x0001e> 24634 in <filename unknown>:0 
  at CanvasSomaticCaller.SomaticCaller.ModelOverallCoverageAndPurity (Int64 genomeLength, CanvasSomaticClusteringMode clusteringMode) <0x414c0000 + 0x013c0> in <filename unknown>:0 
  at CanvasSomaticCaller.SomaticCaller.CallCNVUsingSNVFrequency (Nullable`1 localSDmertic, System.String referenceFolder, CanvasSomaticClusteringMode clusteringMode) <0x414b8720 + 0x00163> in <filename unknown>:0 
  at CanvasSomaticCaller.SomaticCaller.CallVariants (System.String inFile, System.String variantFrequencyFile, System.String outputVCFPath, System.String referenceFolder, System.String name, Nullable`1 localSDmertic, CanvasSomaticClusteringMode clusteringMode) <0x414b4180 + 0x004cf> in <filename unknown>:0 
[ERROR] FATAL UNHANDLED EXCEPTION: System.ArgumentOutOfRangeException: Index was out of range. Must be non-negative and less than the size of the collection.
Parameter name: index
  at System.ThrowHelper.ThrowArgumentOutOfRangeException () <0x7fa81a500d10 + 0x00034> in <filename unknown>:0 
  at System.Collections.Generic.List`1[T].get_Item (Int32 index) <0x7fa81a723ed0 + 0x0001e> 24634 in <filename unknown>:0 
  at CanvasSomaticCaller.SomaticCaller.ModelOverallCoverageAndPurity (Int64 genomeLength, CanvasSomaticClusteringMode clusteringMode) <0x414c0000 + 0x013c0> in <filename unknown>:0 
  at CanvasSomaticCaller.SomaticCaller.CallCNVUsingSNVFrequency (Nullable`1 localSDmertic, System.String referenceFolder, CanvasSomaticClusteringMode clusteringMode) <0x414b8720 + 0x00163> in <filename unknown>:0 
  at CanvasSomaticCaller.SomaticCaller.CallVariants (System.String inFile, System.String variantFrequencyFile, System.String outputVCFPath, System.String referenceFolder, System.String name, Nullable`1 localSDmertic, CanvasSomaticClusteringMode clusteringMode) <0x414b4180 + 0x004cf> in <filename unknown>:0

Hi,

I've been analysing tumour-normal-paired exome sequencing data using Canvas 1.11.0 on Tumor-normal-enrichment mode. This has been conducted on a dilution series of samples to simulate a range of different levels of tumour purity (i.e. from 100% tumour all the way down to 5% tumour).

At a sample tumour purity of >20% Canvas does a reasonably good job of estimating tumour purity, however it does not seem to be able to estimate tumour purity levels <20%. The final estimate always appears to bottom-out at ##EstimatedTumorPurity=0.20, even if the actual purity of the sample is much lower.

I was hoping that somebody could shed some light on this situation. Is it a feature of the program that it simply will not attempt to estimate low tumour purity samples? Are purity estimates below 0.20 possible?

Could this phenomena be related to the filtering of MAFs > 0.1 as part of the CanvasSomaticCaller in an effort to remove putative homozygous positions? If so, is there a way of avoiding this filter?

I've scoured the documentation however I cannot reconcile this issue.

Thank you for help.

After installing canvas I verified this with the example dataset and it worked like a charm. But then I tried to use my own data and I got an error without report. I tried to run the command which produced the error and got the following:

Unhandled Exception:
System.OutOfMemoryException: Out of memory
at (wrapper alloc) System.Object:AllocVector (intptr,intptr)
at SequencingFiles.BamReader.Read (System.Byte[]& data, UInt32 dataLength) <0x41b7b980 + 0x0006a> in :0
at SequencingFiles.BamReader.GetNextAlignment (SequencingFiles.BamAlignment& alignment, Boolean skipAdditionalParsing) <0x41b7f480 + 0x000a3> in :0
at SequencingFiles.BamReader.Jump (Int32 refID, Int32 position) <0x41b7c300 + 0x00373> in :0
at CanvasBin.CanvasBin.LoadObservedAlignmentsBAM (System.String bamFile, Boolean isPairedEnd, System.String chromosome, CanvasCoverageMode coverageMode, CanvasBin.HitArray observed, System.Int16[] fragmentLengths) <0x41b795b0 + 0x0011b> in :0
at CanvasBin.CanvasBin.BinOneGenomicInterval (CanvasBin.CanvasBinParameters parameters, System.Collections.Generic.Dictionary2 possibleAlignments, System.Collections.Generic.Dictionary2 observedAlignments, System.Collections.Generic.Dictionary2 fragmentLengths) <0x41b77aa0 + 0x0011b> in <filename unknown>:0 at CanvasBin.CanvasBin.Run (CanvasBin.CanvasBinParameters parameters) <0x41b76e90 + 0x00233> in <filename unknown>:0 at CanvasBin.Program.Main (System.String[] args) <0x41b47d50 + 0x000e3> in <filename unknown>:0 [ERROR] FATAL UNHANDLED EXCEPTION: System.OutOfMemoryException: Out of memory at (wrapper alloc) System.Object:AllocVector (intptr,intptr) at SequencingFiles.BamReader.Read (System.Byte[]& data, UInt32 dataLength) <0x41b7b980 + 0x0006a> in <filename unknown>:0 at SequencingFiles.BamReader.GetNextAlignment (SequencingFiles.BamAlignment& alignment, Boolean skipAdditionalParsing) <0x41b7f480 + 0x000a3> in <filename unknown>:0 at SequencingFiles.BamReader.Jump (Int32 refID, Int32 position) <0x41b7c300 + 0x00373> in <filename unknown>:0 at CanvasBin.CanvasBin.LoadObservedAlignmentsBAM (System.String bamFile, Boolean isPairedEnd, System.String chromosome, CanvasCoverageMode coverageMode, CanvasBin.HitArray observed, System.Int16[] fragmentLengths) <0x41b795b0 + 0x0011b> in <filename unknown>:0 at CanvasBin.CanvasBin.BinOneGenomicInterval (CanvasBin.CanvasBinParameters parameters, System.Collections.Generic.Dictionary2 possibleAlignments, System.Collections.Generic.Dictionary2 observedAlignments, System.Collections.Generic.Dictionary2 fragmentLengths) <0x41b77aa0 + 0x0011b> in :0
at CanvasBin.CanvasBin.Run (CanvasBin.CanvasBinParameters parameters) <0x41b76e90 + 0x00233> in :0
at CanvasBin.Program.Main (System.String[] args) <0x41b47d50 + 0x000e3> in :0

Why does the test set work and my own with a much smaller bam (only about 2.3 Gb) not? I used the same reference files as in the test setting, only changed the bam...

Hi again,
I see in your paper that you have some promising results for FFPE data when using your software. Is there anything special needed to engage the FFPE processing, or do the regular commands include the same processing steps?

Hello,
the paper says that: "To benchmark the germline workflow, a reference CNV call set for NA12878 individual from the PG family was created by selecting the pedigree-consistent set of deletion calls made using a range of structural variant calling tools."
But I can't find the reference set in the EvaluateCNV folder of the Canvas GitHub repository.
Is that publicly available?
Thanks a lot in advance.
Kind Regards.
-- Jacopo

We're using custom targeted sequencing from a different company than Illumina. They don't provide us with a Nextera manifest formatted file, but I was able to get things to run and get some results by performing some editing, and awk/perl/etc. to make a file that at least looks like an example manifest file I've seen online. It would be much easier to deal with if the --manifest parameter could accept a standard BED file in addition to the proprietary Nextera Manifest format.

Hi again,

I'm doing some test regarding the ploidy and tumour purity estimation. In the design document I see this:

If we did not assign many CNVs (.....), then this SNV-estimated purity is what gets reported to the purity output VCF file

and I see this in my SomaticCNV-a.stdout.txt file

Loaded 3423 somatic variants; saved 3368 somatic SNV frequencies
Estimated tumor purity of 0.410252243280411 from somatic SNV calls
Purity estimates: 1.0000 from CNVs, 0.4103 from SNVs
Fraction abnormal CNV is 0.0407

but my VCF file says

EstimatedTumorPurity=1.00

Am I missing something or should my tumour purity estimate be 0.4103 in the VCF file?

I try to download GenomeSize.xml and filter13.bed from https://illumina.box.com/CanvasPublic into WORKDIR/testing/hg19/, but i can't open it.Can you send those files to me?Thank you very much! ( [email protected])

Hi, I posted on SEQanswers about this error:
ERROR: Canvas workflow error: Illumina.SecondaryAnalysis.JobFailedException: mono returned error code -1

Attached are the Log and Error files. Thank you for your help.
CanvasError.txt
CanvasLog.txt

I have a set of samples from a mouse cancer cell lines sequenced using Illumina HiSeq (exome capture) in addition to a wild type reference (2 replicates of each WT/Cancer).

The purpose is to extract possible CNVs. I have only bam files mapped with BWA and the corresponding genome reference data (mm9).

The first question would be, would you recommend CANVAS for CNV calls from such mouse cell line samples?

If yes, this would lead to the next set of questions:

1- I guess the “Tumor-normal-enrichment” workflow should be used. Right?
2- What should be the --manifest= option in this case? The same as in the github demo?
3- Is providing a filter (-f) required? I have no specifics here for my experiement. Any recommendations?
4- “--b-allele-vcf” I did not get what should I fill in for this parameter.
5- What kind of custom parameters should I add?
6- The “-m” parameter is found in the demo but not in the actual help of CANVAS? What is its usage?

How can I limit the number of threads to use by Canvas? This is important in shared environments such as HPC clusters.

Hi

I was just wondering, can you use Canvas to detect copy number variants from any WGS data? The manual and publication talks almost explicitly about tumor and normal samples. Shouldn't e.g. Somatic-WGS (CNV calling of a somatic sample from whole genome sequencing data) mode be apt for any human somatic-WGS data?

Can Canvas be used for detecting CNVs in constitutional diseases with WES data?
Basically, we expect a smaller fold change in copy number in constitutional diseases than in somatic samples. What is the Limit of Detection (LOD) of Canvas? is it able to detect a single copy of gain/loss?

Hi, is there a tool that allows for the robust merging of CNV calls for more than one individual?

I have a trio and want to combine the CNV calls generated by Canvas for each individual into a common one.

What is the best approach here?

Hi,

I am running CANVAS on WES data and getting the error at CanvasSomaticCaller.exe step.Please find the SomaticCNV-WES_65324.stderr.txt as an attachment.

Thanks
Shruti Kapil
SomaticCNV-WES_65324.stderr.txt

Hi

I am wondering the main difference between Manta and Canvas. I've got the literatures for both and actually Manta user for a large dataset. My understanding is Canvas takes a bin-based approach (RD method?) .. Also, the supplementary document of Canvas has few benchmark tables but no comparison with Manta. Just wondering how the performance is different between two tools.

Thanks

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?

/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 
5/26/2016,10:10:39.729,Running Canvas Somatic-WGS 1.3.9.0
5/26/2016,10:10:39.730,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
5/26/2016,10:10:40.249,Running checkpoint 1: 'CanvasSNV'
5/26/2016,10:10:40.284,Running checkpoint 2: 'CanvasBin'
5/26/2016,10:10:40.640,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" 
5/26/2016,10:10:40.640,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" 
5/26/2016,10:10:40.640,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" 
5/26/2016,10:10:40.640,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" 
5/26/2016,10:10:40.640,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" 
5/26/2016,10:10:40.640,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" 
5/26/2016,10:10:40.641,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" 
5/26/2016,10:10:40.641,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" 
5/26/2016,10:19:52.911,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" 
5/26/2016,10:21:33.514,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" 
5/26/2016,10:26:48.713,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" 
5/26/2016,10:29:11.423,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" 
5/26/2016,10:31:13.998,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" 
5/26/2016,10:31:48.709,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" 
5/26/2016,10:32:00.968,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" 
5/26/2016,10:32:49.648,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" 
5/26/2016,10:33:00.067,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" 
5/26/2016,10:35:05.512,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" 
5/26/2016,10:37:33.932,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" 
5/26/2016,10:38:55.683,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" 
5/26/2016,10:39:29.808,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" 
5/26/2016,10:39:39.565,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" 
5/26/2016,10:40:31.859,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" 
5/26/2016,10:40:40.170,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" 
5/26/2016,10:43:25.457,Max job memory (GB): 2.4
5/26/2016,10:43:25.457,Longest job runtime (Hours): 0.37
5/26/2016,10:43:25.463,DoWorkParallelThreads, attempt 1 of 1
5/26/2016,10:43:25.463,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 
5/26/2016,10:57:35.898,Max job memory (GB): 22.8
5/26/2016,10:57:35.898,Longest job runtime (Hours): 0.24
5/26/2016,10:57:35.899,Elapsed time (step/time(sec)/name)   2   00:46:55.6  CanvasBin
5/26/2016,10:57:35.899,Saving checkpoint results to /projects/rcorbettprj2/CNV_2016/Canvas/out/Checkpoints/02-CanvasBin.json
5/26/2016,10:57:36.447,Running checkpoint 3: 'CanvasClean'
5/26/2016,10:57:36.631,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"
5/26/2016,10:58:34.192,Max job memory (GB): 1.9
5/26/2016,10:58:34.193,Longest job runtime (Hours): 0.02
5/26/2016,10:58:34.193,Elapsed time (step/time(sec)/name)   3   00:00:57.7  CanvasClean
5/26/2016,10:58:34.193,Saving checkpoint results to /projects/rcorbettprj2/CNV_2016/Canvas/out/Checkpoints/03-CanvasClean.json
5/26/2016,10:58:34.280,Running checkpoint 4: 'CanvasPartition'
5/26/2016,10:58:34.286,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" 
5/26/2016,10:59:14.586,Max job memory (GB): 1.8
5/26/2016,10:59:14.586,Longest job runtime (Hours): 0.01
5/26/2016,10:59:14.586,Elapsed time (step/time(sec)/name)   4   00:00:40.3  CanvasPartition
5/26/2016,10:59:14.586,Saving checkpoint results to /projects/rcorbettprj2/CNV_2016/Canvas/out/Checkpoints/04-CanvasPartition.json
5/26/2016,10:59:14.610,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

Hi,

Canvas tells me it cannot find 'mono', but it is the right path.

. OS: Linux

. Downloaded Canvas binaries (not built from source)

. Downloaded all reference files (except 'dbsnp.vcf') from BaseSpace and placed then in '$HOME/lib/Canvas_1.11.0/ref_files/'

. The following command works:
$HOME/lib/mono-4.6.1/bin/mono $HOME/lib/Canvas_1.11.0/Canvas.exe -h

. The following command does NOT work (Error_log attached):
$HOME/lib/mono-4.6.1/bin/mono $HOME/lib/Canvas_1.11.0/Canvas.exe
Tumor-normal-enrichment
--bam=$HOME/tumor.bam
--normal-bam=$HOME/normal.bam
--reference=$HOME/lib/Canvas_1.11.0/ref_files/kmer.fa
--manifest=$HOME/lib/Canvas_1.11.0/ref_files/targets_Canvas.txt
--genome-folder=$HOME/lib/Canvas_1.11.0/ref_files/
--sample-name=TEST
--filter-bed=$HOME/lib/Canvas_1.11.0/ref_files/filter13.bed
--output=$HOME/Canvas/test
--b-allele-vcf=$HOME/normal_snps_indels.g.vcf
--custom-parameters=CanvasBin,-m=TruncatedDynamicRange

I get the error after 'Running checkpoint 1: 'CanvasSNV''

Any idea what could be wrong?
Thanks !

CanvasError.txt

To make it easier to run on container-aware linux distributions, it might be good to distribute a Docker Image or at least a Dockerfile.

FROM mono

RUN mkdir /canvas

COPY * /canvas/

ENTRYPOINT ["mono", "/canvas/Canvas.exe"]

CMD ["--help"]

Hi there,

I'm trying to get Canvas 1.25 working. I gather from the docs that this new version requires .NET instead of mono.

I installed the .Net Core and tried running Canvas with this command:

/opt/dotnet/shared/Microsoft.NETCore.App/1.1.2/dotnet Canvas.dll
Error: assembly specified in the dependencies manifest was not found -- package: 'combinatorics', version: '1.0.0', path: 'Combinatorics.dll'

Obfiously, I'm new to the .NET side of things. Do you have any tips? I tried searching my .NET install for the combinatorics dll, but didn't find anything. Is it part of canvas?

I know that bin size means something a little different in Canvas ("the number of unique
genomic k-mers per bin"), but is it possible to set a fixed physical window size, e.g. 10 kb, which is what most CNV detection algorithms do. They just count reads within these windows.

In SoftwareDesignDocument.pdf it says: "CanvasBin supports user-defined bins specified by -n ." But I actually tried this with 50 kb windows and Canvas didn't run. The file format was:

chr1 0 50000
chr1 50000 100000
chr1 100000 150000

etc.

May I know how I can perform CNV calling of a tumor/normal pair from whole-genome sequencing data with the current version of the software? Thanks

Dear Development Team,

The chromosome notation in my bam file is 1,2,3 ..., which does not match the default of the notation in Canvas: chr1,chr2,chr3.... After manually changing the command from chr1 to 1, the CanvasSNV.dll worked.

I wonder if possible to change this default in Canvas. If not, would it be possible to send me the full list of commands that Canvas.dll would generate. I could use that as a template to generate my own commands.

Thank you. I will appreciate your help.
Best,
Shan

Trying to run the Somatic-Enrichment workflow. Getting the following error:

17/08/2016,15:24:00.636,ERROR: Canvas workflow error: System.BadImageFormatException: An attempt was made to load a program with an incorrect format. (Exception from HRESULT: 0x8007000B)
at SequencingFiles.Compression.SafeNativeMethods.UncompressBlock(Byte[] compressedBlock, UInt32 compressedLen, Byte[] uncompressedBlock, UInt32 uncompressedLen)
at SequencingFiles.BamReader.ReadBlock()
at SequencingFiles.BamReader.Read(Byte[]& data, UInt32 dataLength)
at SequencingFiles.BamReader.LoadHeaderData()
at SequencingFiles.BamReader.Open(Stream inStream)
at SequencingFiles.BamReader.Open(String filename)
at Isas.Shared.Bam.LoadIsPairedEnd()
at Illumina.SecondaryAnalysis.CanvasRunner.InvokeCanvasBin(CanvasCallset callset, String canvasReferencePath, String canvasBedPath, String ploidyBedPath) in D:\TeamCity\buildAgent\work\7ce21c24b500a92f\Src\Canvas\Canvas\CanvasRunner.cs:line 126
at Illumina.SecondaryAnalysis.CanvasRunner.<>c__DisplayClass17_0.b__1() in D:\TeamCity\buildAgent\work\7ce21c24b500a92f\Src\Canvas\Canvas\CanvasRunner.cs:line 528
at Isas.Shared.Checkpointing.CheckpointRunnerAsync.CheckpointHelper1.<WrapWithBenchmark>b__9_0() at Isas.Shared.Checkpointing.CheckpointRunnerAsync.CheckpointHelper1.b__10_0()
at Isas.Shared.Checkpointing.CheckpointRunnerAsync.CheckpointHelper1.<WrapWithStopCheckpointCheck>b__12_0() at System.Threading.Tasks.Task1.InnerInvoke()
at System.Threading.Tasks.Task.Execute()
--- End of stack trace from previous location where exception was thrown ---
at System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(Task task)
at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(Task task)
at Isas.Shared.Checkpointing.CheckpointRunnerAsync.RunCheckpoint[TOut](String key, Func`1 function)
at Illumina.SecondaryAnalysis.CanvasRunner.d__17.MoveNext() in D:\TeamCity\buildAgent\work\7ce21c24b500a92f\Src\Canvas\Canvas\CanvasRunner.cs:line 528
--- End of stack trace from previous location where exception was thrown ---
at System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(Task task)
at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(Task task)
at Illumina.SecondaryAnalysis.CanvasRunner.CallSample(CanvasCallset callset) in D:\TeamCity\buildAgent\work\7ce21c24b500a92f\Src\Canvas\Canvas\CanvasRunner.cs:line 498
at Canvas.ModeLauncher.Launch() in D:\TeamCity\buildAgent\work\7ce21c24b500a92f\Src\Canvas\Canvas\ModeLauncher.cs:line 61

From trying CanvasBin separately, there seems to be a problem loading the Bam file. My Bam files validated with picard validatesamfile. Not sure what the problem is? The Bam files were aligned with bwa, and the reference used in alignment included GL chromosomes, not sure if that is causing the problem? The chromosome names in the Bam file, the reference fasta and the manifest are all in the same format.

Thank you.

Cheers,
Peter

Any idea what might be causing this?
* Error deriving purity estimate from somatic SNVs. Details: System.Collections.Generic.KeyNotFoundException: The given key was not present in the dictionary. at System.ThrowHelper.ThrowKeyNotFoundException () <0x7f0227c98970 + 0x00015> in <filename unknown>:0 at System.Collections.Generic.Dictionary2[TKey,TValue].get_Item (System.Collections.Generic.TKey key) <0x7f0227b0e3e0 + 0x0004a> in :0
at CanvasSomaticCaller.SomaticCaller.EstimatePurityFromSomaticSNVs () <0x41177660 + 0x00329> in :0
at CanvasSomaticCaller.SomaticCaller.CallCNVUsingSNVFrequency (Nullable1 localSDmertic, System.String referenceFolder) <0x4114eea0 + 0x00273> in <filename unknown>:0

How does Canvas deal with sub-clonal events in WGS samples? Is there anyway to get that information from the Canvas output if there are sub-clonal events present?

Thanks,
Minita

I'm a new Mono user, long time bioinformatics software user/installer. Maybe for the benefit of the community you could provide a Linux bundle so end users don't need Mono installed?

On multiprocessor machines with sufficient memory we do not expect any single Canvas step to take more than 2.5 hours. However, if you are encountering this issue you can workaround it by modifying Canvas.exe.config as follows (increasing to 10 hours maximum):

<?xml version="1.0"?>
<configuration>
  <appSettings>
    <add key="MaximumHoursPerProcess" value="10"/>
  </appSettings>
  <startup> 
    <supportedRuntime version="v4.0" sku=".NETFramework,Version=v4.5.1"/>
  </startup>
</configuration>

Hey there,
I don't see an option to include the aligned reads from the matched normal to help normalize the depths of the tumour read counts. It does show up in your example of the "Tumor-normal-enrichment" command. In my experience, having the matched normal helped normalize out some biases in read coverage that weren't properly modeled by GC, etc. Is there a way to include the normal read depths when running "somatic-WGS" ?

thanks,
RIchard

In the Weaver LITE last step (taken up from Weaver github)
Weaver LITE -f SIMU.fa -S FINAL_SV -s SNP -g REGION -w X.bam.wig -r 0 -m map100mer.bd -p 64 -t 20 -n 0

What are -t and -n values?
I am running Weaver for whole exome sequencing data and there is only one sample and no control, only single sample. What are the values that need to be entered in -t and -n option and how can I get these values?

Hello all,
I'm running Somatic Canvas, but I keep getting the following error. Do you know what is this about?
---Failed command:
mono-4.4.0/bin/mono canvas-1.3.9/CanvasBin.exe

--- both stdout and stderr log files are empty!
at Illumina.SecondaryAnalysis.JobManager.CheckExitCodes (System.Collections.Generic.List`1 jobs, Boolean throwExceptionOnBadExitCode) <0x411493b0 + 0x004eb> in :0

Do we have mono/Linux executable (Canvas.exe) for the latest version 1.25.0?
Looks, we don't see Canvas.exe in Canvas-1.25_x64.tar.gz.
Thanks and Regards,
Naga

I have a reference genome that I'm trying to generate GenomeSize.xml for. Looking at a few other issues on here, I see there's no standalone tool used to generate this file, so I'm doing it manually, but I'm confused about the "md5" field. In the example file, the md5 is different for all chromosomes, but they all come from the same reference genome file. Please let me know what this "md5" field refers to.

Thanks,
Raymon

The following error occurs when attempting run "Somatic-WGS". Any idea how to solve it?

2016-11-20,19:36:24.224,ERROR: Canvas workflow error: Isas.Shared.JobFailedException: mono returned error code -1

---Failed command:
/sw/comp/mono/3.12.0/milou/bin/mono /pica/h1/xkajoa/bin/1.11.0/CanvasBin.exe -b "/home/xkajoa/b2013029/INBOX/P4951/P4951_104/03-BAM/P4951_104.clean.dedup.bam" -p -r "/home/xkajoa/private/GRCh37/WholeGenomeFasta/genome.fa" -c 1 -m GCContentWeighted -f "/home/xkajoa/private/GRCh37/filter13.bed" -d 100 -o "/home/xkajoa/private/canvas_104/TempCNV_104/104_0_1.dat"

--- both stdout and stderr log files are empty!

I'm running Canvas on Linux (Scientific Linux release 6.8), with the following mono version:

Mono JIT compiler version 3.12.0 (tarball Fri Jan 16 10:29:56 CET 2015)
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

(Unfortunately I can't try out any more recent version of Mono, if that is what might cause the problem, since I don't have root access on this server)

CanvasError.txt
CanvasLog.txt

Nearly all of my germline data is from whole exome sequencing, and I was wondering if it would be possible to use your software to detect variants in exome data. From the documentation it looks like there is only a WGS (not exome) option for germline samples. Do you know if there is a way around this that might enable me to use your software?

Just clarifying, if I only want to analyze a single chromosome of interest, I passed the --chr=chr19 to CanvasBin.exe. But reading the doc, do I also have to -i param with the chrom specific .dat file?

Tried to download GRCh38 reference files from https://illumina.box.com/CanvasPublic. Error message is- "files do not exist or you do not have permissions to access this folder".

I was able to download hg19 input files a couple of months back, not sure if the file permissions were changed after that..

Thanks
Kshithija

I'm trying to prepare a mouse reference genome for canvas, but so far cannot figure out how to build FlagUniqueKmers.csproj using xbuild under mono. Some better documentation around this area would help me quite a bit.