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Canvas - Copy number variant (CNV) calling from DNA sequencing data
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Commandline parsing error #132

Closed DaGaMs closed 4 years ago

DaGaMs commented 4 years ago

Hi,

I've tried running the following command:

dotnet ~/Code/Canvas-1.40.0.1613+master_x64/Canvas.dll SmallPedigree-WGS -b Processed/bam/P11-A11_trim_mCtoT_md.bam --proband=Processed/bam/P11-A11_trim_mCtoT_md.bam --population-b-allele-vcf=Data/canvas_files/dbsnp.vcf --reference=Data/canvas_files/genome.fa --genome-folder=Data/canvas_files --filter-bed=Data/canvas_files/filter13.bed --output=Processed/canvas/

but whatever I do, I get this error:

2019-10-08T17:22:14+01:00, 
2019-10-08T17:22:14+01:00,Running checkpoint 01: Validate input
2019-10-08T17:22:14+01:00,ERROR: Exception caught in WorkDoerFactory. Cancelling all jobs. Exception: 
        Type specified in JSON 'CanvasCommon.CommandLineParsing.OptionProcessing.FailedParsingResult`1[[Canvas.CommandLineParsing.GermlineWgsInput, Canvas, Version=1.40.0.1613, Culture=neutral, PublicKeyToken=null]], CanvasCommon, Version=1.40.0.1613, Culture=neutral, PublicKeyToken=null' is not compatible with 'CanvasCommon.CommandLineParsing.OptionProcessing.IParsingResult`1[[Canvas.CommandLineParsing.SmallPedigreeInput, Canvas, Version=1.40.0.1613, Culture=neutral, PublicKeyToken=null]], CanvasCommon, Version=1.40.0.1613, Culture=neutral, PublicKeyToken=null'. Path '$type', line 2, position 151.
Newtonsoft.Json.JsonSerializationException: Type specified in JSON 'CanvasCommon.CommandLineParsing.OptionProcessing.FailedParsingResult`1[[Canvas.CommandLineParsing.GermlineWgsInput, Canvas, Version=1.40.0.1613, Culture=neutral, PublicKeyToken=null]], CanvasCommon, Version=1.40.0.1613, Culture=neutral, PublicKeyToken=null' is not compatible with 'CanvasCommon.CommandLineParsing.OptionProcessing.IParsingResult`1[[Canvas.CommandLineParsing.SmallPedigreeInput, Canvas, Version=1.40.0.1613, Culture=neutral, PublicKeyToken=null]], CanvasCommon, Version=1.40.0.1613, Culture=neutral, PublicKeyToken=null'. Path '$type', line 2, position 151.
   at Newtonsoft.Json.Serialization.JsonSerializerInternalReader.ResolveTypeName(JsonReader reader, Type& objectType, JsonContract& contract, JsonProperty member, JsonContainerContract containerContract, JsonProperty containerMember, String qualifiedTypeName)
   at Newtonsoft.Json.Serialization.JsonSerializerInternalReader.ReadMetadataProperties(JsonReader reader, Type& objectType, JsonContract& contract, JsonProperty member, JsonContainerContract containerContract, JsonProperty containerMember, Object existingValue, Object& newValue, String& id)
   at Newtonsoft.Json.Serialization.JsonSerializerInternalReader.CreateObject(JsonReader reader, Type objectType, JsonContract contract, JsonProperty member, JsonContainerContract containerContract, JsonProperty containerMember, Object existingValue)
   at Newtonsoft.Json.Serialization.JsonSerializerInternalReader.Deserialize(JsonReader reader, Type objectType, Boolean checkAdditionalContent)
   at Newtonsoft.Json.JsonSerializer.DeserializeInternal(JsonReader reader, Type objectType)
   at Newtonsoft.Json.JsonConvert.DeserializeObject(String value, Type type, JsonSerializerSettings settings)
   at Newtonsoft.Json.JsonConvert.DeserializeObject[T](String value, JsonSerializerSettings settings)
   at Isas.Framework.Checkpointing.Internals.CheckpointJsonSerializer.Deserialize[T](IFileLocation path)
   at Isas.Framework.Checkpointing.Internals.CheckpointJsonSerializer.Load[T](String checkpoint)
   at Isas.Framework.Checkpointing.Internals.CoreCheckpointRunner.RunCheckpoint[TResult](String name, Func`2 run)
   at Canvas.CommandLineParsing.ModeParser`1.Parse(MainParser main, ILogger logger, ISettings settings, ICheckpointRunner checkpointRunner, IWorkDoer workDoer, String[] args, TextWriter standardWriter, TextWriter errorWriter)
   at Canvas.CommandLineParsing.MainParser.<>c__DisplayClass20_2.<Run>b__2(ICheckpointRunner checkpointer)
   at Isas.Framework.Checkpointing.CheckpointerFactory.<>c__DisplayClass1_1.<RunWithCheckpointer>b__1(CheckpointManager checkpointManager)
   at Isas.Framework.Utilities.IArgumentSupplierExtensions.<>c__DisplayClass0_0`2.<SupplyArgument>b__1(TFill arg)
   at Isas.Framework.Checkpointing.Internals.CheckpointManagerFactory.<>c__DisplayClass4_0`1.<SupplyArgument>b__0()
   at Isas.Framework.Utilities.IArgumentSupplierExtensions.<>c__DisplayClass0_0`2.<SupplyArgument>b__0()
   at Isas.Framework.Utilities.IArgumentSupplierExtensions.<>c__DisplayClass0_0`2.<SupplyArgument>b__1(TFill arg)
   at Isas.Framework.Utilities.TaskTrackerFactory.<>c__DisplayClass2_0`1.<SupplyArgument>b__0()
   at Isas.Framework.Utilities.IArgumentSupplierExtensions.<>c__DisplayClass0_0`2.<SupplyArgument>b__0()
   at Isas.Framework.WorkManagement.JobLaunching.JobLauncherFactory.RunWithJobLauncher(ILogger logger, ISettings settings, IDirectoryLocation loggingDir, Action`1 logCommand, CancellationToken cancellationToken, Action`1 function)
   at Isas.Framework.WorkManagement.JobLaunching.JobLauncherFactory.RunWithJobLauncher(ILogger logger, ISettings settings, IDirectoryLocation analysisFolder, CancellationToken cancellationToken, Action`1 function)
   at Isas.Framework.WorkManagement.ResourceManagement.WorkResourceManagerFactory.RunWithResourceManager(ILogger logger, ISettings settings, CancellationToken cancellationToken, Action`1 function)
   at Isas.Framework.WorkManagement.WorkDoerFactory.RunWithWorkDoer(ILogger logger, ISettings settings, IDirectoryLocation analysisFolder, CancellationTokenSource cancellationTokenSource, Action`1 function)
   at Isas.Framework.FrameworkFactory.IsasFrameworkFactory.RunWithLogger(IFileLocation workflowLog, IFileLocation workflowError, Action`1 function)
   at Canvas.CommandLineParsing.MainParser.Run(String[] args, TextWriter standardOutput, TextWriter standardError)
   at Canvas.Program.Main(String[] args)

Any idea what I'm doing wrong? This is running on a fairly old Scientific Linux 6 cluster.

DaGaMs commented 4 years ago

So, interestingly, when I removed the -f option, I got an error message about missing SM tag in the bam header. I fixed that, and I got an error about the missing -f option. When I put the -f option back, I get the same error as above. So, maybe something wrong with the -f argument parsing?!

eroller commented 4 years ago

Try using an empty output directory. I think the error is getting cached as part of our resume from checkpoint functionality.

DaGaMs commented 4 years ago

Indeed, that did the trick. Thanks!