Adding repeats track fails for hs1 genome reference

[olegs]

[Jul 7, 2023 11:11:29] ERROR PathExtensions Repeats: processing /Users/Oleg.Shpynov/.jbr_browser/genomes/hs1/rmsk.txt.gz: [FAILED] after 1.406 ms
Caused by: ERROR NullPointerException
org.jetbrains.bio.genome.Repeats$repeatsPath$1.invoke(Annotations.kt:72)
org.jetbrains.bio.genome.Repeats$repeatsPath$1.invoke(Annotations.kt:60)
org.jetbrains.bio.util.PathExtensionsKt$checkOrRecalculate$1$1$block$1.invoke(PathExtensions.kt:348)
org.jetbrains.bio.util.PathExtensionsKt$checkOrRecalculate$1$1$block$1.invoke(PathExtensions.kt:347)
org.jetbrains.bio.util.PathExtensionsKt$checkOrRecalculate$1$1.invoke(PathExtensions.kt:490)
org.jetbrains.bio.util.PathExtensionsKt$checkOrRecalculate$1$1.invoke(PathExtensions.kt:345)
org.jetbrains.bio.util.LoggerExtensionsKt.time(LoggerExtensions.kt:20)
org.jetbrains.bio.util.PathExtensionsKt.checkOrRecalculate(PathExtensions.kt:345)
org.jetbrains.bio.util.PathExtensionsKt.checkOrRecalculate$default(PathExtensions.kt:320)
org.jetbrains.bio.genome.Repeats.repeatsPath(Annotations.kt:60)
org.jetbrains.bio.genome.Repeats.all$lambda-1(Annotations.kt:85)
com.google.common.cache.LocalCache$LocalManualCache$1.load(LocalCache.java:4876)
com.google.common.cache.LocalCache$LoadingValueReference.loadFuture(LocalCache.java:3529)
com.google.common.cache.LocalCache$Segment.loadSync(LocalCache.java:2278)
com.google.common.cache.LocalCache$Segment.lockedGetOrLoad(LocalCache.java:2155)
com.google.common.cache.LocalCache$Segment.get(LocalCache.java:2045)
com.google.common.cache.LocalCache.get(LocalCache.java:3951)
com.google.common.cache.LocalCache$LocalManualCache.get(LocalCache.java:4871)
org.jetbrains.bio.genome.Repeats.all$bioinf_commons(Annotations.kt:84)
org.jetbrains.bio.genome.Chromosome.getRepeats(Genome.kt:557)
org.jetbrains.bio.browser.tracks.base.RepeatsTrackView$preprocess$repeatClasses$1.invoke(RepeatsTrackView.kt:37)
org.jetbrains.bio.browser.tracks.base.RepeatsTrackView$preprocess$repeatClasses$1.invoke(RepeatsTrackView.kt:35)
kotlin.sequences.FlatteningSequence$iterator$1.ensureItemIterator(Sequences.kt:315)
kotlin.sequences.FlatteningSequence$iterator$1.hasNext(Sequences.kt:303)
kotlin.sequences.SequencesKt___SequencesKt.toCollection(_Sequences.kt:786)
kotlin.sequences.SequencesKt___SequencesKt.toSet(_Sequences.kt:827)
org.jetbrains.bio.browser.tracks.base.RepeatsTrackView.preprocess(RepeatsTrackView.kt:38)
org.jetbrains.bio.browser.GenomeBrowser$preprocess$2.invoke(GenomeBrowser.kt:279)
org.jetbrains.bio.browser.GenomeBrowser$preprocess$2.invoke(GenomeBrowser.kt:277)
org.jetbrains.bio.util.LoggerExtensionsKt.time(LoggerExtensions.kt:20)
org.jetbrains.bio.browser.GenomeBrowser.preprocess(GenomeBrowser.kt:277)
org.jetbrains.bio.browser.GenomeBrowser.access$preprocess(GenomeBrowser.kt:32)
org.jetbrains.bio.browser.GenomeBrowser$preprocess$asTasks$1.invoke$lambda-1$lambda-0(GenomeBrowser.kt:232)
java.base/java.util.concurrent.ForkJoinTask$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)
[Jul 7, 2023 11:11:29] ERROR GenomeBrowser Failed to preprocess track Repeats
Caused by: ERROR UncheckedExecutionException java.lang.NullPointerException
com.google.common.cache.LocalCache$Segment.get(LocalCache.java:2051)
com.google.common.cache.LocalCache.get(LocalCache.java:3951)
com.google.common.cache.LocalCache$LocalManualCache.get(LocalCache.java:4871)
org.jetbrains.bio.genome.Repeats.all$bioinf_commons(Annotations.kt:84)
org.jetbrains.bio.genome.Chromosome.getRepeats(Genome.kt:557)
org.jetbrains.bio.browser.tracks.base.RepeatsTrackView$preprocess$repeatClasses$1.invoke(RepeatsTrackView.kt:37)
org.jetbrains.bio.browser.tracks.base.RepeatsTrackView$preprocess$repeatClasses$1.invoke(RepeatsTrackView.kt:35)
kotlin.sequences.FlatteningSequence$iterator$1.ensureItemIterator(Sequences.kt:315)
kotlin.sequences.FlatteningSequence$iterator$1.hasNext(Sequences.kt:303)
kotlin.sequences.SequencesKt___SequencesKt.toCollection(_Sequences.kt:786)
kotlin.sequences.SequencesKt___SequencesKt.toSet(_Sequences.kt:827)
org.jetbrains.bio.browser.tracks.base.RepeatsTrackView.preprocess(RepeatsTrackView.kt:38)
org.jetbrains.bio.browser.GenomeBrowser$preprocess$2.invoke(GenomeBrowser.kt:279)
org.jetbrains.bio.browser.GenomeBrowser$preprocess$2.invoke(GenomeBrowser.kt:277)
org.jetbrains.bio.util.LoggerExtensionsKt.time(LoggerExtensions.kt:20)
org.jetbrains.bio.browser.GenomeBrowser.preprocess(GenomeBrowser.kt:277)
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:232)
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)

[olegs]

I've cleaned cache ~/.jbr_browser folder and repeated everything from scratch. It worked good.
My hypothesis is that probably some of the downloaded files were truncated and this can be the cause of NPE.

[olegs]

Closing as cannot reproduce anymore.