Closed malnirav closed 2 years ago
Can you also provide the index file *.jsi?
I have created a bug for this: https://nirvana-annotator.atlassian.net/browse/NIR-976.
It seems that Jasix is crashing if the query range is outside of what is present in the file. From your query it seems like you are trying to get all entries for chr11. A better way to do that is:
jasix --in outputs/example.annot.json.gz -q 11
Ahh gotcha. Thanks
Did a quick check and the position it hangs up on is chr11:1017710
$ gzcat example.annot.json.gz | grep '1017710'
{"chromosome":"chr11","position":1017710,"refAllele":"G","altAlleles":["T"],"quality":292.16,"filters":["PASS"],"cytogeneticBand":"11p15.5","variants":[{"vid":"11-1017710-G-T","chromosome":"chr11","begin":1017710,"end":1017710,"refAllele":"G","altAllele":"T","variantType":"SNV","hgvsg":"NC_000011.9:g.1017710G>T","phylopScore":-4.1,"cosmic":[{"id":"COSM5765441","refAllele":"G","altAllele":"T","gene":"MUC6","sampleCount":1,"cancerTypesAndCounts":[{"cancerType":"carcinoma","count":1}],"cancerSitesAndCounts":[{"cancerSite":"large intestine","count":1}],"isAlleleSpecific":true},{"id":"COSM5765442","refAllele":"G","altAllele":"T","gene":"MUC6_ENST00000421673","sampleCount":1,"cancerTypesAndCounts":[{"cancerType":"carcinoma","count":1}],"cancerSitesAndCounts":[{"cancerSite":"large intestine","count":1}],"isAlleleSpecific":true}],"dbsnp":["rs113964902"],"gnomad":{"coverage":526,"failedFilter":true,"allAf":0.000103,"allAn":242510,"allAc":25,"allHc":0,"afrAf":0.001424,"afrAn":13346,"afrAc":19,"afrHc":0,"amrAf":0,"amrAn":33114,"amrAc":0,"amrHc":0,"easAf":0,"easAn":17224,"easAc":0,"easHc":0,"finAf":0,"finAn":20720,"finAc":0,"finHc":0,"nfeAf":0.000053,"nfeAn":112810,"nfeAc":6,"nfeHc":0,"asjAf":0,"asjAn":9898,"asjAc":0,"asjHc":0,"sasAf":0,"sasAn":29462,"sasAc":0,"sasHc":0,"othAf":0,"othAn":5936,"othAc":0,"othHc":0,"maleAf":0.00003,"maleAn":132838,"maleAc":4,"maleHc":0,"femaleAf":0.000191,"femaleAn":109672,"femaleAc":21,"femaleHc":0,"controlsAllAf":0.000029,"controlsAllAn":103708,"controlsAllAc":3},"primateAI":[{"hgnc":"MUC6","scorePercentile":0.23}],"revel":{"score":0.021},"topmed":{"allAf":0.368868,"allAn":125568,"allAc":46318,"allHc":0,"failedFilter":true},"transcripts":[{"transcript":"ENST00000421673.2","source":"Ensembl","bioType":"protein_coding","codons":"caC/caA","aminoAcids":"H/Q","cdnaPos":"5142","cdsPos":"5091","exons":"31/33","proteinPos":"1697","geneId":"ENSG00000184956","hgnc":"MUC6","consequence":["missense_variant"],"hgvsc":"ENST00000421673.2:c.5091C>A","hgvsp":"ENSP00000406861.2:p.(His1697Gln)","isCanonical":true,"polyPhenScore":0,"polyPhenPrediction":"benign","proteinId":"ENSP00000406861.2","siftScore":0.7,"siftPrediction":"tolerated - low confidence"},{"transcript":"NM_005961.2","source":"RefSeq","bioType":"protein_coding","codons":"caC/caA","aminoAcids":"H/Q","cdnaPos":"5142","cdsPos":"5091","exons":"31/33","proteinPos":"1697","geneId":"4588","hgnc":"MUC6","consequence":["missense_variant"],"hgvsc":"NM_005961.2:c.5091C>A","hgvsp":"NP_005952.2:p.(His1697Gln)","isCanonical":true,"polyPhenScore":0,"polyPhenPrediction":"benign","proteinId":"NP_005952.2","siftScore":0.7,"siftPrediction":"tolerated - low confidence"},{"transcript":"ENST00000532016.1","source":"Ensembl","bioType":"protein_coding","geneId":"ENSG00000184956","hgnc":"MUC6","consequence":["upstream_gene_variant"],"proteinId":"ENSP00000433246.1"},{"transcript":"ENST00000527242.1","source":"Ensembl","bioType":"protein_coding","geneId":"ENSG00000184956","hgnc":"MUC6","consequence":["downstream_gene_variant"],"proteinId":"ENSP00000436903.1"}]}]},
$ dotnet Nirvana/v3.17/Jasix.dll --in example.annot.json.gz -q 11:1017710
{"positions":[
ERROR: Error reading JObject from JsonReader. Path '', line 0, position 0.
Stack trace:
at Newtonsoft.Json.Linq.JObject.Load(JsonReader reader, JsonLoadSettings settings)
at Newtonsoft.Json.Linq.JObject.Parse(String json, JsonLoadSettings settings)
at Newtonsoft.Json.Linq.JObject.Parse(String json)
at Jasix.DataStructures.Utilities.PrintJsonEntry(String entry, Boolean needComma, StreamWriter writer) in /home/mstromberg/NirvanaIllumina/Jasix/DataStructures/Utilities.cs:line 53
at Jasix.QueryProcessor.PrintLargeVariantsExtendingIntoQuery(ValueTuple`3 query) in /home/mstromberg/NirvanaIllumina/Jasix/QueryProcessor.cs:line 123
at Jasix.QueryProcessor.ProcessQuery(IEnumerable`1 queryStrings, Boolean printHeader) in /home/mstromberg/NirvanaIllumina/Jasix/QueryProcessor.cs:line 95
at Jasix.JasixMain.ProgramExecution() in /home/mstromberg/NirvanaIllumina/Jasix/JasixMain.cs:line 129
at CommandLine.Builders.ConsoleAppErrors.Execute(Func`1 executeMethod) in /home/mstromberg/NirvanaIllumina/CommandLine/Builders/ConsoleAppBuilder.cs:line 162
Issue has been fixed in the 3.18.1 release.
@rajatshuvro Thank you for fixing the problem reported above in 3.18.1
Seeing another error with Jasix on a different test sample:
$ dotnet Nirvana/v3.17/Jasix.dll --in test.annot.json.gz --query "chr1:231293288-232485615"
{"positions":[
ERROR: Found an invalid header when reading the GZip block ((stream))
Stack trace:
at Compression.FileHandling.BlockGZipStream.ReadBlock() in /home/mstromberg/NirvanaIllumina/Compression/FileHandling/BlockGZipStream.cs:line 153
at Compression.FileHandling.BlockGZipStream.SeekVirtualFilePointer(UInt64 virtualPosition) in /home/mstromberg/NirvanaIllumina/Compression/FileHandling/BlockGZipStream.cs:line 252
at Compression.FileHandling.BlockGZipStream.set_Position(Int64 value) in /home/mstromberg/NirvanaIllumina/Compression/FileHandling/BlockGZipStream.cs:line 56
at Jasix.QueryProcessor.RepositionReader(Int64 location) in /home/mstromberg/NirvanaIllumina/Jasix/QueryProcessor.cs:line 154
at Jasix.QueryProcessor.ReadOverlappingJsonLines(ValueTuple`3 query)+MoveNext() in /home/mstromberg/NirvanaIllumina/Jasix/QueryProcessor.cs:line 191
at Jasix.QueryProcessor.PrintAllVariantsFromQueryBegin(ValueTuple`3 query, Boolean needComma) in /home/mstromberg/NirvanaIllumina/Jasix/QueryProcessor.cs:line 108
at Jasix.QueryProcessor.ProcessQuery(IEnumerable`1 queryStrings, Boolean printHeader) in /home/mstromberg/NirvanaIllumina/Jasix/QueryProcessor.cs:line 96
at Jasix.JasixMain.ProgramExecution() in /home/mstromberg/NirvanaIllumina/Jasix/JasixMain.cs:line 129
at CommandLine.Builders.ConsoleAppErrors.Execute(Func`1 executeMethod) in /home/mstromberg/NirvanaIllumina/CommandLine/Builders/ConsoleAppBuilder.cs:line 162
Files are available here to reproduce the error:
Given this annotated json: https://github.com/malnirav/data_share/blob/main/example.annot.json.gz
What causing the hiccup in Jasix for the query range below?