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JetBrains-Research / jbr

JBR Genome Browser
https://doi.org/10.1093/bioinformatics/btab376
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Exception while loading SPAN 1.0 models into JBR latest version #174

Closed olegs closed 2 years ago

olegs commented 2 years ago 
[Jan 14, 2022 14:17:10] ERROR GenomeBrowser Failed to preprocess track GSM646318_GM12878_H3K27me3_rep1_GSM646332_GM12878_Input_rep1_200#d3379
Caused by: ERROR IllegalStateException File /Users/Oleg.Shpynov/.jbr_browser/cache/coverage_GSM646332_GM12878_Input_rep1_unique#e06dd.npz doesn't contain data for chrUn_gl000248.
org.jetbrains.bio.genome.coverage.SingleEndCoverage$Companion.load$bioinf_commons(SingleEndCoverage.kt:175)
org.jetbrains.bio.genome.coverage.Coverage$Companion.load$bioinf_commons(Coverage.kt:64)
org.jetbrains.bio.genome.query.ReadsQuery.coverage(ReadsQuery.kt:65)
org.jetbrains.bio.genome.query.ReadsQuery.getUncached(ReadsQuery.kt:34)
org.jetbrains.bio.genome.query.ReadsQuery.getUncached(ReadsQuery.kt:26)
org.jetbrains.bio.genome.query.CachingInputQuery$get$1.invoke(InputQuery.kt:36)
org.jetbrains.bio.util.LockManager.synchronized(LockManager.kt:39)
org.jetbrains.bio.genome.query.CachingInputQuery.get(InputQuery.kt:32)
org.jetbrains.bio.span.coverage.CoverageScoresQuery.<init>(CoverageScoresQuery.kt:60)
org.jetbrains.bio.span.fit.Span1AnalyzeFitInformation.prepareScores(Span1AnalyzeFitInformation.kt:80)
org.jetbrains.bio.browser.span.SpanModelTrackView.preprocess(SpanModelTrackView.kt:87)
org.jetbrains.bio.browser.GenomeBrowser$preprocess$2.invoke(GenomeBrowser.kt:373)
org.jetbrains.bio.browser.GenomeBrowser$preprocess$2.invoke(GenomeBrowser.kt:371)
org.jetbrains.bio.util.LoggerExtensionsKt.time(LoggerExtensions.kt:20)
org.jetbrains.bio.browser.GenomeBrowser.preprocess(GenomeBrowser.kt:371)
org.jetbrains.bio.browser.GenomeBrowser.access$preprocess(GenomeBrowser.kt:32)
org.jetbrains.bio.browser.GenomeBrowser$preprocess$asTasks$1.invoke$lambda-1$lambda-0(GenomeBrowser.kt:326)
java.base/java.util.concurrent.ForkJoinTask$AdaptedCallable.exec(ForkJoinTask.java:1428)
java.base/java.util.concurrent.ForkJoinTask.doExec$$$capture(ForkJoinTask.java:373)
java.base/java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java)
java.base/java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(ForkJoinPool.java:1182)
java.base/java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1655)
java.base/java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1622)
java.base/java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:165)
[Jan 14, 2022 14:17:10] Preprocessing track 'GSM646318_GM12878_H3K27me3_rep1_GSM646332_GM12878_Input_rep1_200#d3379': done in 4.351 min
[Jan 14, 2022 14:17:10] Preprocessing: 100% (1/1), Elapsed time: 4 min 21 s [done]
[Jan 14, 2022 14:17:19] [1/1] Loading file:/Users/Oleg.Shpynov/Desktop/2021_GSE26320_copy/fit/GSM646320_GM12878_H3K36me3_rep1_GSM646332_GM12878_Input_rep1_200%2313990.span as SPAN
[Jan 14, 2022 14:17:19] 'Loading files': Preprocessing 1 tracks
[Jan 14, 2022 14:17:19] Preprocessing track 'GSM646320_GM12878_H3K36me3_rep1_GSM646332_GM12878_Input_rep1_200#13990'...
[Jan 14, 2022 14:17:19] Loading model: /Users/Oleg.Shpynov/Desktop/2021_GSE26320_copy/fit/GSM646320_GM12878_H3K36me3_rep1_GSM646332_GM12878_Input_rep1_200#13990.span
[Jan 14, 2022 14:17:20] Completed loading model: /Users/Oleg.Shpynov/Desktop/2021_GSE26320_copy/fit/GSM646320_GM12878_H3K36me3_rep1_GSM646332_GM12878_Input_rep1_200#13990.span
olegs commented 2 years ago

Fixed in https://github.com/JetBrains-Research/bioinf-commons/commit/94e42fe3385fbea4d72d4948a88851873ef334ed