Unhandled Exception: System.IndexOutOfRangeException: Index was outside the bounds of the array.

[BenoitFiset]

Hi Eric,

As you know, using mono and TN with 1.11.0 of canvas.... Trying to adjust files for WES and getting these errors.

These errors are in all the dat.stderr.txt files. Where do I start to debug this ?

A full error sample:

Unhandled Exception:
System.IndexOutOfRangeException: Index was outside the bounds of the array.
at CanvasBin.CanvasBin.ExcludeTagsOverlappingFilterFile (System.String filterFile, System.Collections.Generic.IDictionary`2[TKey,TValue] tags) [0x0001a] in <63fa03d6c0824
e34bfc976c23685abf9>:0 
  at CanvasBin.CanvasBin.BinOneGenomicInterval (CanvasBin.CanvasBinParameters parameters, System.Collections.Generic.Dictionary`2[TKey,TValue] possibleAlignments, System.Co
llections.Generic.Dictionary`2[TKey,TValue] observedAlignments, System.Collections.Generic.Dictionary`2[TKey,TValue] fragmentLengths) [0x0007f] in <63fa03d6c0824e34bfc976c2
3685abf9>:0 
  at CanvasBin.CanvasBin.Run (CanvasBin.CanvasBinParameters parameters) [0x00040] in <63fa03d6c0824e34bfc976c23685abf9>:0 
  at CanvasBin.Program.Main (System.String[] args) [0x0003b] in <63fa03d6c0824e34bfc976c23685abf9>:0 
[ERROR] FATAL UNHANDLED EXCEPTION: System.IndexOutOfRangeException: Index was outside the bounds of the array.
  at CanvasBin.CanvasBin.ExcludeTagsOverlappingFilterFile (System.String filterFile, System.Collections.Generic.IDictionary`2[TKey,TValue] tags) [0x0001a] in <63fa03d6c0824
e34bfc976c23685abf9>:0 
  at CanvasBin.CanvasBin.BinOneGenomicInterval (CanvasBin.CanvasBinParameters parameters, System.Collections.Generic.Dictionary`2[TKey,TValue] possibleAlignments, System.Co
llections.Generic.Dictionary`2[TKey,TValue] observedAlignments, System.Collections.Generic.Dictionary`2[TKey,TValue] fragmentLengths) [0x0007f] in <63fa03d6c0824e34bfc976c2
3685abf9>:0 
  at CanvasBin.CanvasBin.Run (CanvasBin.CanvasBinParameters parameters) [0x00040] in <63fa03d6c0824e34bfc976c23685abf9>:0 
  at CanvasBin.Program.Main (System.String[] args) [0x0003b] in <63fa03d6c0824e34bfc976c23685abf9>:0 

Thanks,

B.

[BenoitFiset]

Hi Eric,

Seems I found it.... My --filter-bed file had spaces instead of TABS between columns....
Canvas now seems to be humming fine... I'll see later if finishes...

To be updated later...

[BenoitFiset]

This seems the right fix.

Closing

[osowiecki]

I think my problem is similar in nature. My ploidy.vcf fails but switching from spaces to tabs doesn't fix the problem.

I copied the header from my Germline Strelka result vcf file and placed information about chromosome X in male at the bottom.

#########################################
...
##FILTER=<ID=LowDepth,Description="Locus depth is below 3">
##FILTER=<ID=NotGenotyped,Description="Locus contains forcedGT input alleles which could not be genotyped">
##FILTER=<ID=PloidyConflict,Description="Genotype call from variant caller not consistent with chromosome ploidy">
##FILTER=<ID=NoPassedVariantGTs,Description="No samples at this locus pass all sample filters and have a variant genotype">
##bcftools_filterVersion=1.9+htslib-1.9
##bcftools_filterCommand=filter --exclude 'QUAL<30 || GQ<30' ./vcf/CF_6942/CF_6942_strelka.vcf.gz; Date=Tue Jun 25 00:59:17 2019
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CF_6942
X 0 . N . PASS END=123869142 CN 1

#########################################

I get this error :

#########################################

2019-06-25T01:08:43+02:00,ERROR: Exception caught in WorkDoerFactory. Cancelling all jobs. Exception: Index was outside the bounds of the array. System.IndexOutOfRangeException: Index was outside the bounds of the array. at Isas.SequencingFiles.Vcf.VcfReader.ConvertColumnsToVariant(String[] cols, VcfVariant variant, String& genotypeTagString, String[ ]& genotypeTagOrder, Int32 numSamples) at Isas.SequencingFiles.Vcf.VcfReader.GetNextVariant(VcfVariant& variant) at CanvasCommon.PloidyInfo.LoadPloidyFromVcfFile(String vcfPath, Int32 sampleIndex) in D:\TeamCity\buildAgent\work\a29a190a11771d97 \Src\Canvas\CanvasCommon\PloidyInfo.cs:line 132 at CanvasPedigreeCaller.SampleMetrics.GetSampleInfo(IReadOnlyList1 segments, String ploidyBedPath, Int32 numberOfTrimmedBins, Samp
leId id)
at CanvasPedigreeCaller.CanvasPedigreeCaller.CallVariants(List1 variantFrequencyFiles, List1 segmentFiles, IFileLocation outVcfFi
le, String ploidyBedPath, String referenceFolder, List1 sampleNames, String commonCnvsBedPath, List1 sampleTypes) in D:\TeamCity\bui
ldAgent\work\a29a190a11771d97\Src\Canvas\CanvasPedigreeCaller\CanvasPedigreeCaller.cs:line 93
at CanvasPedigreeCaller.Program.<>c__DisplayClass2_0.b__12(IWorkDoer workDoer) in D:\TeamCity\buildAgent\work\a29a190a11771d97
\Src\Canvas\CanvasPedigreeCaller\Program.cs:line 191
at Isas.Framework.WorkManagement.JobLaunching.JobLauncherFactory.RunWithJobLauncher(ILogger logger, ISettings settings, IDirectoryL
ocation loggingDir, Action1 logCommand, CancellationToken cancellationToken, Action1 function)
at Isas.Framework.WorkManagement.JobLaunching.JobLauncherFactory.RunWithJobLauncher(ILogger logger, ISettings settings, IDirectoryL
ocation analysisFolder, CancellationToken cancellationToken, Action1 function) at Isas.Framework.WorkManagement.ResourceManagement.WorkResourceManagerFactory.RunWithResourceManager(ILogger logger, ISettings set tings, CancellationToken cancellationToken, Action1 function)
at Isas.Framework.WorkManagement.WorkDoerFactory.RunWithWorkDoer(ILogger logger, ISettings settings, IDirectoryLocation analysisFol
der, CancellationTokenSource cancellationTokenSource, Action1 function) at CanvasPedigreeCaller.Program.Run(String[] args) in D:\TeamCity\buildAgent\work\a29a190a11771d97\Src\Canvas\CanvasPedigreeCaller\ Program.cs:line 193 at CanvasPedigreeCaller.Program.Main(String[] args) in D:\TeamCity\buildAgent\work\a29a190a11771d97\Src\Canvas\CanvasPedigreeCaller \Program.cs:line 39

#########################################

By the way, can I use my filtered Strelka Germline result for one normal sample as a --sample-b-allele-vcf file? The dbsnp.vcf for my species (dog) crash complaining that dbsnp file doesn't contain a genotype column.

[osowiecki]

Ok. Seems that the ploidy file needs to be in range of variants present in strelka2 output.
My starting position in chromosome X wasn't 0 like in example but somewhere down the line as my strelka2 Germline vcf contains all chromosomes in one file.

I extracted minimal and maximal position of X chromosome from vcf file and not Canvas worked on my male sample.

`
bcftools filter --exclude 'QUAL<30 || GQ<30' ./vcf/CF_132/CF_132_strelka.vcf.gz > ./temp.vcf
cat ./temp.vcf | grep '#|PASS' > temp2.vcf
cat ./temp2.vcf | grep "#" > head.vcf
cat ./head.vcf > ./data/ploidy.vcf

#MALE

zless ./temp2.vcf | grep -P "X\t" > test_p
a=$(cat ./test_p | cut -d$'\t' -f2 |sort -V | head -n1)
b=$(cat ./test_p | cut -d$'\t' -f2 |sort -V | tail -n1)
printf "X\t${a}\t.\tN\t\t.\tPASS\tEND=${b}\tCN\t1\n" > ./m
cat ./head.vcf ./m> ./data/male.vcf

Canvas SmallPedigree-WGS -b ./bam/CF_36.bam --sample-b-allele-vcf=./temp2.vcf -o ./CNV/CF_36 -r ./data/kmers.fasta -g ./data/canFam3/ --filter-bed=./data/filter.bed --ploidy-vcf=./data/male.vcf
`