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Failed to create arithmetic track view #191

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olegs opened this issue Aug 10, 2023 · 1 comment
Open

Failed to create arithmetic track view #191

olegs opened this issue Aug 10, 2023 · 1 comment
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bug Something isn't working

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@olegs
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olegs commented Aug 10, 2023

[10 Aug 2023 16:01:34] Session /Users/Oleg.Shpynov/data/2023_GSE26320/2023_gse26320_hg38_k36me3_Nhek_rep2.yaml loaded
2023-08-10 16:01:52.313 java[27792:14695709] +[CATransaction synchronize] called within transaction
[10 Aug 2023 16:02:07] DEBUG ProgressDialog Init progress log appender
[10 Aug 2023 16:02:07] [1/2] Loading file:/Users/Oleg.Shpynov/data/2023_GSE26320_rnaseq/NHEK_rep2_hg38_minus_ENCFF602ENH.bigWig as BIGWIG
[10 Aug 2023 16:02:07] DEBUG TrackViewLoader [1/2] Loading file:/Users/Oleg.Shpynov/data/2023_GSE26320_rnaseq/NHEK_rep2_hg38_minus_ENCFF602ENH.bigWig as BIGWIG {
  
}
[10 Aug 2023 16:02:07] [2/2] Loading file:/Users/Oleg.Shpynov/data/2023_GSE26320_rnaseq/NHEK_rep2_hg38_plus_ENCFF506SFB.bigWig as BIGWIG
[10 Aug 2023 16:02:07] DEBUG TrackViewLoader [2/2] Loading file:/Users/Oleg.Shpynov/data/2023_GSE26320_rnaseq/NHEK_rep2_hg38_plus_ENCFF506SFB.bigWig as BIGWIG {
  
}
[10 Aug 2023 16:02:07] 'Loading files': Preprocessing 2 tracks
[10 Aug 2023 16:02:07] Preprocessing: 50% (1/2), Elapsed time: 5 ms
[10 Aug 2023 16:02:07] Preprocessing: 100% (2/2), Elapsed time: 6 ms, Throughput: 3 ms/item, ETA: 0 ns [done]
[10 Aug 2023 16:02:07] DEBUG ProgressDialog Detach progress log appender
2023-08-10 16:02:20.989 java[27792:14695709] +[CATransaction synchronize] called within transaction
[10 Aug 2023 16:02:48] DEBUG ProgressDialog Init progress log appender
[10 Aug 2023 16:02:48] 'Adding arithmetic tracks': Preprocessing 1 tracks
[10 Aug 2023 16:02:48] DEBUG PathExtensions NHEK_rep2_hg38_ENCFF602ENH.bigWig [Sum]: File is missing: /Users/Oleg.Shpynov/data/2023_GSE26320_rnaseq/NHEK_rep2_hg38_ENCFF602ENH.bigWig.bw
[10 Aug 2023 16:02:48] NHEK_rep2_hg38_ENCFF602ENH.bigWig [Sum]: processing /Users/Oleg.Shpynov/data/2023_GSE26320_rnaseq/NHEK_rep2_hg38_ENCFF602ENH.bigWig.bw...
[10 Aug 2023 16:02:48] NHEK_rep2_hg38_ENCFF602ENH.bigWig [Sum]: [sum] load bigwig data: 0% (1/910), Elapsed time: 21 ms
[10 Aug 2023 16:02:48] NHEK_rep2_hg38_ENCFF602ENH.bigWig [Sum]: [sum] calc values: 0% (1/455), Elapsed time: 22 ms
[10 Aug 2023 16:02:49] NHEK_rep2_hg38_ENCFF602ENH.bigWig [Sum]: [sum] calc values: 100% (455/455), Elapsed time: 81 ms, Throughput: 5 items/ms, ETA: 0 ns [done]
[10 Aug 2023 16:02:49] NHEK_rep2_hg38_ENCFF602ENH.bigWig [Sum]: [sum] load bigwig data: 100% (910/910), Elapsed time: 80 ms, Throughput: 88 μs/item, ETA: 0 ns [done]
[10 Aug 2023 16:02:49] ERROR PathExtensions NHEK_rep2_hg38_ENCFF602ENH.bigWig [Sum]: processing /Users/Oleg.Shpynov/data/2023_GSE26320_rnaseq/NHEK_rep2_hg38_ENCFF602ENH.bigWig.bw: [FAILED] after 86.24 ms
Caused by: ERROR IllegalStateException java.lang.IllegalStateException: Files '/Users/Oleg.Shpynov/data/2023_GSE26320_rnaseq/NHEK_rep2_hg38_minus_ENCFF602ENH.bigWig' and '/Users/Oleg.Shpynov/data/2023_GSE26320_rnaseq/NHEK_rep2_hg38_plus_ENCFF506SFB.bigWig' expected to have same. BedGraph structure, but it isn't true for chromosome: hg38:chr9_KI270720v1_random
java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)
java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:562)
java.base/java.util.concurrent.ForkJoinTask.reportException(ForkJoinTask.java:591)
java.base/java.util.concurrent.ForkJoinTask.invoke(ForkJoinTask.java:689)
java.base/java.util.stream.ReduceOps$ReduceOp.evaluateParallel(ReduceOps.java:927)
java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:233)
java.base/java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:682)
org.jetbrains.bio.browser.tracks.arithmetics.ArithmeticTrackView$createBigWigArithmeticTrack$2.invoke(ArithmeticTrackView.kt:212)
org.jetbrains.bio.browser.tracks.arithmetics.ArithmeticTrackView$createBigWigArithmeticTrack$2.invoke(ArithmeticTrackView.kt:192)
org.jetbrains.bio.util.PathExtensionsKt$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.browser.tracks.arithmetics.ArithmeticTrackView.createBigWigArithmeticTrack(ArithmeticTrackView.kt:192)
org.jetbrains.bio.browser.tracks.arithmetics.ArithmeticTrackView$newTrack$2.preprocessSrc(ArithmeticTrackView.kt:279)
org.jetbrains.bio.browser.tracks.big.BigWigTrackView.preprocess(BigWigTrackView.kt:141)
org.jetbrains.bio.browser.GenomeBrowser$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$lambda-0(GenomeBrowser.kt:232)
org.jetbrains.bio.browser.GenomeBrowser.preprocess(GenomeBrowser.kt:268)
org.jetbrains.bio.browser.desktop.DesktopGenomeBrowser$addAndProcessNewTracks$1.invoke(DesktopGenomeBrowser.kt:351)
org.jetbrains.bio.browser.desktop.DesktopGenomeBrowser$addAndProcessNewTracks$1.invoke(DesktopGenomeBrowser.kt:347)
org.jetbrains.bio.browser.desktop.dialogs.ProgressDialog$display$block$1.invoke$lambda-1(ProgressDialog.kt:173)
java.base/java.lang.Thread.run(Thread.java:833)
[10 Aug 2023 16:02:49] ERROR GenomeBrowser Failed to preprocess track NHEK_rep2_hg38_ENCFF602ENH.bigWig [Sum]
Caused by: ERROR IllegalStateException java.lang.IllegalStateException: Files '/Users/Oleg.Shpynov/data/2023_GSE26320_rnaseq/NHEK_rep2_hg38_minus_ENCFF602ENH.bigWig' and '/Users/Oleg.Shpynov/data/2023_GSE26320_rnaseq/NHEK_rep2_hg38_plus_ENCFF506SFB.bigWig' expected to have same. BedGraph structure, but it isn't true for chromosome: hg38:chr9_KI270720v1_random
java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)
java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:562)
java.base/java.util.concurrent.ForkJoinTask.reportException(ForkJoinTask.java:591)
java.base/java.util.concurrent.ForkJoinTask.invoke(ForkJoinTask.java:689)
java.base/java.util.stream.ReduceOps$ReduceOp.evaluateParallel(ReduceOps.java:927)
java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:233)
java.base/java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:682)
org.jetbrains.bio.browser.tracks.arithmetics.ArithmeticTrackView$createBigWigArithmeticTrack$2.invoke(ArithmeticTrackView.kt:212)
org.jetbrains.bio.browser.tracks.arithmetics.ArithmeticTrackView$createBigWigArithmeticTrack$2.invoke(ArithmeticTrackView.kt:192)
org.jetbrains.bio.util.PathExtensionsKt$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.browser.tracks.arithmetics.ArithmeticTrackView.createBigWigArithmeticTrack(ArithmeticTrackView.kt:192)
org.jetbrains.bio.browser.tracks.arithmetics.ArithmeticTrackView$newTrack$2.preprocessSrc(ArithmeticTrackView.kt:279)
org.jetbrains.bio.browser.tracks.big.BigWigTrackView.preprocess(BigWigTrackView.kt:141)
org.jetbrains.bio.browser.GenomeBrowser$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$lambda-0(GenomeBrowser.kt:232)
org.jetbrains.bio.browser.GenomeBrowser.preprocess(GenomeBrowser.kt:268)
org.jetbrains.bio.browser.desktop.DesktopGenomeBrowser$addAndProcessNewTracks$1.invoke(DesktopGenomeBrowser.kt:351)
org.jetbrains.bio.browser.desktop.DesktopGenomeBrowser$addAndProcessNewTracks$1.invoke(DesktopGenomeBrowser.kt:347)
org.jetbrains.bio.browser.desktop.dialogs.ProgressDialog$display$block$1.invoke$lambda-1(ProgressDialog.kt:173)
java.base/java.lang.Thread.run(Thread.java:833)
[10 Aug 2023 16:02:49] Preprocessing: 100% (1/1), Elapsed time: 139 ms [done]
[10 Aug 2023 16:02:49] DEBUG ProgressDialog Detach progress log appender

@olegs olegs added the bug Something isn't working label Aug 10, 2023
@olegs
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olegs commented Aug 10, 2023

Important to check option 'Input tracks are BedGraph based *.bw tracks with same intervals structure'!

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