Closed BenoitFiset closed 6 years ago
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...
This seems the right fix.
Closing
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.
######################################### ...
X 0 . N
#########################################
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(IReadOnlyList
1 segments, String ploidyBedPath, Int32 numberOfTrimmedBins, Samp
leId id)
at CanvasPedigreeCaller.CanvasPedigreeCaller.CallVariants(List1 variantFrequencyFiles, List
1 segmentFiles, IFileLocation outVcfFi
le, String ploidyBedPath, String referenceFolder, List1 sampleNames, String commonCnvsBedPath, List
1 sampleTypes) in D:\TeamCity\bui
ldAgent\work\a29a190a11771d97\Src\Canvas\CanvasPedigreeCaller\CanvasPedigreeCaller.cs:line 93
at CanvasPedigreeCaller.Program.<>c__DisplayClass2_0.
at Isas.Framework.WorkManagement.JobLaunching.JobLauncherFactory.RunWithJobLauncher(ILogger logger, ISettings settings, IDirectoryL
ocation loggingDir, Action1 logCommand, CancellationToken cancellationToken, Action
1 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, Action
1 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.
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
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
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 `
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:
Thanks,
B.