Details
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Bug
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Status: Resolved
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Major
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Resolution: Fixed
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Capacitor 1.2.1 (API 1.18)
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None
Description
The capacitor crashes with the following message when started with a .bed file. The bed file that causes the problem is attached.
[LEARN] Scanning the input and getting the attributes. profiling [WARN] skipped line 1 protein_coding start_codon 69091 69093 . + . transcript_id "ENST00000335137"; gene_biotype "protein_coding"; 1 "protein_coding start_codon 69091 69093 . + 0 gene_id "ENSG00000186092"; transcript_name "OR4F5-001"; gene_name "OR4F5"; exon_number "1"; [ERROR] Error while iterating loci: java.lang.NumberFormatException: Unable to parse 1 to an integer! at barna.commons.ByteArrayCharSequence.parseInt(ByteArrayCharSequence.java:889) at barna.model.bed.BEDMapping.getNextBlockSize(BEDMapping.java:395) at barna.model.bed.BEDMapping.getLength(BEDMapping.java:458) at barna.flux.capacitor.reconstruction.FluxCapacitor$LocusSolver.learn(FluxCapacitor.java:920) at barna.flux.capacitor.reconstruction.FluxCapacitor$LocusSolver.run(FluxCapacitor.java:242) at barna.flux.capacitor.reconstruction.FluxCapacitor.solve(FluxCapacitor.java:2147) at barna.flux.capacitor.reconstruction.FluxCapacitor.explore(FluxCapacitor.java:2679) at barna.flux.capacitor.reconstruction.FluxCapacitor.getProfile(FluxCapacitor.java:2195) at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:1744) at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:76) at barna.commons.launcher.Flux.main(Flux.java:196) java.lang.RuntimeException: java.lang.NumberFormatException: Unable to parse 1 to an integer! at barna.flux.capacitor.reconstruction.FluxCapacitor.explore(FluxCapacitor.java:2732) at barna.flux.capacitor.reconstruction.FluxCapacitor.getProfile(FluxCapacitor.java:2195) at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:1744) at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:76) at barna.commons.launcher.Flux.main(Flux.java:196) Caused by: java.lang.NumberFormatException: Unable to parse 1 to an integer! at barna.commons.ByteArrayCharSequence.parseInt(ByteArrayCharSequence.java:889) at barna.model.bed.BEDMapping.getNextBlockSize(BEDMapping.java:395) at barna.model.bed.BEDMapping.getLength(BEDMapping.java:458) at barna.flux.capacitor.reconstruction.FluxCapacitor$LocusSolver.learn(FluxCapacitor.java:920) at barna.flux.capacitor.reconstruction.FluxCapacitor$LocusSolver.run(FluxCapacitor.java:242) at barna.flux.capacitor.reconstruction.FluxCapacitor.solve(FluxCapacitor.java:2147) at barna.flux.capacitor.reconstruction.FluxCapacitor.explore(FluxCapacitor.java:2679) ... 4 more [FATAL] Error occured during scanning java.lang.NumberFormatException: Unable to parse 1 to an integer! [SOLVE] Deconvolving reads of overlapping transcripts. decomposing [ERROR] Error while iterating loci: java.lang.NullPointerException at barna.model.Gene.getGeneID(Gene.java:899) at barna.model.gff.GFFObject.createGFFObject(GFFObject.java:674) at barna.flux.capacitor.reconstruction.FluxCapacitor$LocusSolver.outputGFF(FluxCapacitor.java:480) at barna.flux.capacitor.reconstruction.FluxCapacitor$LocusSolver.run(FluxCapacitor.java:251) at barna.flux.capacitor.reconstruction.FluxCapacitor.solve(FluxCapacitor.java:2147) at barna.flux.capacitor.reconstruction.FluxCapacitor.explore(FluxCapacitor.java:2681) at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:1750) at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:76) at barna.commons.launcher.Flux.main(Flux.java:196) [ERROR] java.lang.NullPointerException