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OOM error not shown during tracks preprocessing #51

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olegs opened this issue Nov 6, 2018 · 6 comments
Open

OOM error not shown during tracks preprocessing #51

olegs opened this issue Nov 6, 2018 · 6 comments
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@PetrTsurinov

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@olegs
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olegs commented Nov 6, 2018

I've tried to open data set on ATAC-Seq /mnt/stripe/bio/raw-data/geo-samples/PRJNA392905/ - all the span models simultaneously, and JBR didn't open them without any error messages.

[Nov 6, 2018 13:27:32] Completed loading model: /mnt/stripe/bio/raw-data/geo-samples/PRJNA392905/fastq_bams_span/fit/GSM2692178_200#90ca9.span
[Nov 6, 2018 13:27:32] Preprocess track 'GSM2692178_200#90ca9': done in 1.707 min
[Nov 6, 2018 13:27:32] Preprocess track 'GSM2692186_200#7cf7a'...
[Nov 6, 2018 13:27:32] Completed loading model: /mnt/stripe/bio/raw-data/geo-samples/PRJNA392905/fastq_bams_span/fit/GSM2692181_200#02784.span
[Nov 6, 2018 13:27:34] Loading model: /mnt/stripe/bio/raw-data/geo-samples/PRJNA392905/fastq_bams_span/fit/GSM2692186_200#7cf7a.span
[Nov 6, 2018 13:27:34] Preprocess track 'GSM2692181_200#02784': done in 1.737 min
[Nov 6, 2018 13:27:34] Preprocess track 'GSM2692187_200#80af3'...
[Nov 6, 2018 13:27:34] Loading model: /mnt/stripe/bio/raw-data/geo-samples/PRJNA392905/fastq_bams_span/fit/GSM2692187_200#80af3.span
[Nov 6, 2018 13:27:34] Completed loading model: /mnt/stripe/bio/raw-data/geo-samples/PRJNA392905/fastq_bams_span/fit/GSM2692180_200#4ff46.span
[Nov 6, 2018 13:27:34] Preprocess track 'GSM2692180_200#4ff46': done in 1.738 min
[Nov 6, 2018 13:27:34] Preprocess track 'GSM2692188_200#427d6'...
[Nov 6, 2018 13:27:34] Completed loading model: /mnt/stripe/bio/raw-data/geo-samples/PRJNA392905/fastq_bams_span/fit/GSM2692179_200#2e369.span
[Nov 6, 2018 13:27:34] Preprocess track 'GSM2692179_200#2e369': done in 1.739 min
[Nov 6, 2018 13:27:34] Preprocess track 'GSM2692189_200#bad27'...
[Nov 6, 2018 13:27:34] Loading model: /mnt/stripe/bio/raw-data/geo-samples/PRJNA392905/fastq_bams_span/fit/GSM2692189_200#bad27.span
[Nov 6, 2018 13:27:34] Loading model: /mnt/stripe/bio/raw-data/geo-samples/PRJNA392905/fastq_bams_span/fit/GSM2692188_200#427d6.span
[Nov 6, 2018 13:28:10] Completed loading model: /mnt/stripe/bio/raw-data/geo-samples/PRJNA392905/fastq_bams_span/fit/GSM2692184_200#f7013.span
[Nov 6, 2018 13:28:10] Completed loading model: /mnt/stripe/bio/raw-data/geo-samples/PRJNA392905/fastq_bams_span/fit/GSM2692182_200#88f64.span
[Nov 6, 2018 13:28:11] Completed loading model: /mnt/stripe/bio/raw-data/geo-samples/PRJNA392905/fastq_bams_span/fit/GSM2692183_200#2da60.span
[Nov 6, 2018 13:28:11] Preprocess track 'GSM2692182_200#88f64': done in 2.351 min
[Nov 6, 2018 13:28:11] Preprocess track 'GSM2692184_200#f7013': done in 2.293 min
[Nov 6, 2018 13:28:11] Preprocess: 8% (14/180), Elapsed time: 4 min 9 s, Throughput: 3 items/min, ETA: 49 min 18 s
[Nov 6, 2018 13:28:11] Preprocess track 'GSM2692190_200#3cacd'...
[Nov 6, 2018 13:28:11] Preprocess track 'GSM2692191_200#d92dd'...
[Nov 6, 2018 13:28:11] Preprocess track 'GSM2692183_200#2da60': done in 2.351 min
[Nov 6, 2018 13:28:11] Preprocess track 'GSM2692192_200#1c5a6'...
[Nov 6, 2018 13:28:11] Loading model: /mnt/stripe/bio/raw-data/geo-samples/PRJNA392905/fastq_bams_span/fit/GSM2692191_200#d92dd.span
[Nov 6, 2018 13:28:11] Loading model: /mnt/stripe/bio/raw-data/geo-samples/PRJNA392905/fastq_bams_span/fit/GSM2692192_200#1c5a6.span
[Nov 6, 2018 13:28:11] Loading model: /mnt/stripe/bio/raw-data/geo-samples/PRJNA392905/fastq_bams_span/fit/GSM2692190_200#3cacd.span
[Nov 6, 2018 13:29:28] Preprocess track 'GSM2692193_200#2ae6d'...
[Nov 6, 2018 13:29:28] Preprocess track 'GSM2692194_200#50615'...
[Nov 6, 2018 13:29:37] Loading model: /mnt/stripe/bio/raw-data/geo-samples/PRJNA392905/fastq_bams_span/fit/GSM2692194_200#50615.span
[Nov 6, 2018 13:29:37] Loading model: /mnt/stripe/bio/raw-data/geo-samples/PRJNA392905/fastq_bams_span/fit/GSM2692193_200#2ae6d.span
Exception in thread "Thread-29" java.lang.OutOfMemoryError: Java heap space
	at java.nio.HeapByteBuffer.<init>(HeapByteBuffer.java:57)
	at java.nio.ByteBuffer.allocate(ByteBuffer.java:335)
	at org.jetbrains.bio.npy.NpzFile$Reader$getBuffers$1.invoke(Npz.kt:86)
	at org.jetbrains.bio.npy.NpzFile$Reader$getBuffers$1.invoke(Npz.kt:33)
	at kotlin.sequences.GeneratorSequence$iterator$1.calcNext(Sequences.kt:521)
	at kotlin.sequences.GeneratorSequence$iterator$1.hasNext(Sequences.kt:539)
	at kotlin.sequences.SequencesKt___SequencesKt.first(_Sequences.kt:103)
	at org.jetbrains.bio.npy.NpzFile$Reader$introspect$1.invoke(Npz.kt:43)
	at org.jetbrains.bio.npy.NpzFile$Reader$introspect$1.invoke(Npz.kt:33)
	at kotlin.sequences.TransformingSequence$iterator$1.next(Sequences.kt:149)
	at kotlin.sequences.SequencesKt___SequencesKt.toCollection(_Sequences.kt:647)
	at kotlin.sequences.SequencesKt___SequencesKt.toMutableList(_Sequences.kt:677)
	at kotlin.sequences.SequencesKt___SequencesKt.toList(_Sequences.kt:668)
	at org.jetbrains.bio.npy.NpzFile$Reader.introspect(Npz.kt:63)
	at org.jetbrains.bio.dataframe.DataFrameMapper$NPZ.guess(DataFrameMapper.kt:134)
	at org.jetbrains.bio.dataframe.DataFrameMapper.load(DataFrameMapper.kt:28)
	at org.jetbrains.bio.dataframe.DataFrame$Companion.load(DataFrame.kt:226)
	at org.jetbrains.bio.experiments.fit.SpanModelFitExperiment$Companion.loadResults(SpanModelFitExperiment.kt:330)
	at org.jetbrains.bio.browser.span.SpanModelTrackView.preprocessImpl(SpanModelTrackView.kt:73)
	at org.jetbrains.bio.browser.tracks.TrackView.preprocess(TrackView.kt:173)
	at org.jetbrains.bio.browser.GenomeBrowser$preprocess$asTasks$1$$special$$inlined$map$lambda$1.call(GenomeBrowser.kt:286)
	at org.jetbrains.bio.browser.GenomeBrowser$preprocess$asTasks$1$$special$$inlined$map$lambda$1.call(GenomeBrowser.kt:28)
	at com.google.common.util.concurrent.TrustedListenableFutureTask$TrustedFutureInterruptibleTask.runInterruptibly(TrustedListenableFutureTask.java:125)
	at com.google.common.util.concurrent.InterruptibleTask.run(InterruptibleTask.java:57)
	at com.google.common.util.concurrent.TrustedListenableFutureTask.run(TrustedListenableFutureTask.java:78)
	at java.util.concurrent.ForkJoinTask$RunnableExecuteAction.exec(ForkJoinTask.java:1402)
	at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
	at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056)
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)
[Nov 6, 2018 13:29:39 ERROR TrackView] Failed to preprocess track GSM2692190_200#3cacd
Caused by: ERROR ClosedByInterruptException
java.nio.channels.ClosedByInterruptException
	at java.nio.channels.spi.AbstractInterruptibleChannel.end(AbstractInterruptibleChannel.java:202)
	at java.nio.channels.Channels$ReadableByteChannelImpl.read(Channels.java:387)
	at org.jetbrains.bio.npy.NpzFile$Reader$getBuffers$1.invoke(Npz.kt:89)
	at org.jetbrains.bio.npy.NpzFile$Reader$getBuffers$1.invoke(Npz.kt:33)
	at kotlin.sequences.GeneratorSequence$iterator$1.calcNext(Sequences.kt:521)
	at kotlin.sequences.GeneratorSequence$iterator$1.hasNext(Sequences.kt:539)
	at kotlin.sequences.SequencesKt___SequencesKt.first(_Sequences.kt:103)
	at org.jetbrains.bio.npy.NpzFile$Reader$introspect$1.invoke(Npz.kt:43)
	at org.jetbrains.bio.npy.NpzFile$Reader$introspect$1.invoke(Npz.kt:33)
	at kotlin.sequences.TransformingSequence$iterator$1.next(Sequences.kt:149)
	at kotlin.sequences.SequencesKt___SequencesKt.toCollection(_Sequences.kt:647)
	at kotlin.sequences.SequencesKt___SequencesKt.toMutableList(_Sequences.kt:677)
	at kotlin.sequences.SequencesKt___SequencesKt.toList(_Sequences.kt:668)
	at org.jetbrains.bio.npy.NpzFile$Reader.introspect(Npz.kt:63)
	at org.jetbrains.bio.dataframe.DataFrameMapper$NPZ.guess(DataFrameMapper.kt:134)
	at org.jetbrains.bio.dataframe.DataFrameMapper.load(DataFrameMapper.kt:28)
	at org.jetbrains.bio.dataframe.DataFrame$Companion.load(DataFrame.kt:226)
	at org.jetbrains.bio.experiments.fit.SpanModelFitExperiment$Companion.loadResults(SpanModelFitExperiment.kt:330)
	at org.jetbrains.bio.browser.span.SpanModelTrackView.preprocessImpl(SpanModelTrackView.kt:73)
	at org.jetbrains.bio.browser.tracks.TrackView.preprocess(TrackView.kt:173)
	at org.jetbrains.bio.browser.GenomeBrowser$preprocess$asTasks$1$$special$$inlined$map$lambda$1.call(GenomeBrowser.kt:286)
	at org.jetbrains.bio.browser.GenomeBrowser$preprocess$asTasks$1$$special$$inlined$map$lambda$1.call(GenomeBrowser.kt:28)
	at com.google.common.util.concurrent.TrustedListenableFutureTask$TrustedFutureInterruptibleTask.runInterruptibly(TrustedListenableFutureTask.java:125)
	at com.google.common.util.concurrent.InterruptibleTask.run(InterruptibleTask.java:57)
	at com.google.common.util.concurrent.TrustedListenableFutureTask.run(TrustedListenableFutureTask.java:78)
	at java.util.concurrent.ForkJoinTask$RunnableExecuteAction.exec(ForkJoinTask.java:1402)
	at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
	at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056)
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)

[Nov 6, 2018 13:29:39] Preprocess track 'GSM2692190_200#3cacd': done in 1.468 min
[Nov 6, 2018 13:29:39] Preprocess: 9% (17/180), Elapsed time: 5 min 37 s, Throughput: 3 items/min, ETA: 53 min 56 s
[Nov 6, 2018 13:29:49] Completed loading model: /mnt/stripe/bio/raw-data/geo-samples/PRJNA392905/fastq_bams_span/fit/GSM2692185_200#775be.span
[Nov 6, 2018 13:29:49] Preprocess track 'GSM2692185_200#775be': done in 2.324 min
[Nov 6, 2018 13:29:49] Preprocess: 10% (18/180), Elapsed time: 5 min 48 s, Throughput: 3 items/min, ETA: 52 min 14 s
[Nov 6, 2018 13:29:54] Completed loading model: /mnt/stripe/bio/raw-data/geo-samples/PRJNA392905/fastq_bams_span/fit/GSM2692186_200#7cf7a.span
[Nov 6, 2018 13:29:54] Preprocess track 'GSM2692186_200#7cf7a': done in 2.372 min
[Nov 6, 2018 13:29:54] Completed loading model: /mnt/stripe/bio/raw-data/geo-samples/PRJNA392905/fastq_bams_span/fit/GSM2692189_200#bad27.span
[Nov 6, 2018 13:29:54] Preprocess track 'GSM2692189_200#bad27': done in 2.341 min
[Nov 6, 2018 13:29:54] Completed loading model: /mnt/stripe/bio/raw-data/geo-samples/PRJNA392905/fastq_bams_span/fit/GSM2692187_200#80af3.span
[Nov 6, 2018 13:29:54] Preprocess track 'GSM2692187_200#80af3': done in 2.343 min
[Nov 6, 2018 13:29:54] Completed loading model: /mnt/stripe/bio/raw-data/geo-samples/PRJNA392905/fastq_bams_span/fit/GSM2692188_200#427d6.span
[Nov 6, 2018 13:29:54] Preprocess track 'GSM2692188_200#427d6': done in 2.344 min
[Nov 6, 2018 13:30:02 ERROR TrackView] Failed to preprocess track GSM2692193_200#2ae6d
Caused by: ERROR ClosedByInterruptException
java.nio.channels.ClosedByInterruptException
	at java.nio.channels.spi.AbstractInterruptibleChannel.end(AbstractInterruptibleChannel.java:202)
	at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:164)
	at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:65)
	at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:109)
	at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:103)
	at java.io.BufferedInputStream.read1(BufferedInputStream.java:284)
	at java.io.BufferedInputStream.read(BufferedInputStream.java:345)
	at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284)
	at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326)
	at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178)
	at java.io.InputStreamReader.read(InputStreamReader.java:184)
	at java.io.BufferedReader.fill(BufferedReader.java:161)
	at java.io.BufferedReader.read1(BufferedReader.java:212)
	at java.io.BufferedReader.read(BufferedReader.java:286)
	at com.google.gson.stream.JsonReader.fillBuffer(JsonReader.java:1287)
	at com.google.gson.stream.JsonReader.nextNonWhitespace(JsonReader.java:1325)
	at com.google.gson.stream.JsonReader.consumeNonExecutePrefix(JsonReader.java:1567)
	at com.google.gson.stream.JsonReader.doPeek(JsonReader.java:534)
	at com.google.gson.stream.JsonReader.peek(JsonReader.java:425)
	at com.google.gson.Gson.fromJson(Gson.java:883)
	at com.google.gson.Gson.fromJson(Gson.java:825)
	at org.jetbrains.bio.experiments.fit.SpanFitInformation$Companion.load(SpanModelFitExperiment.kt:141)
	at org.jetbrains.bio.experiments.fit.SpanModelFitExperiment$Companion.loadResults(SpanModelFitExperiment.kt:326)
	at org.jetbrains.bio.browser.span.SpanModelTrackView.preprocessImpl(SpanModelTrackView.kt:73)
	at org.jetbrains.bio.browser.tracks.TrackView.preprocess(TrackView.kt:173)
	at org.jetbrains.bio.browser.GenomeBrowser$preprocess$asTasks$1$$special$$inlined$map$lambda$1.call(GenomeBrowser.kt:286)
	at org.jetbrains.bio.browser.GenomeBrowser$preprocess$asTasks$1$$special$$inlined$map$lambda$1.call(GenomeBrowser.kt:28)
	at com.google.common.util.concurrent.TrustedListenableFutureTask$TrustedFutureInterruptibleTask.runInterruptibly(TrustedListenableFutureTask.java:125)
	at com.google.common.util.concurrent.InterruptibleTask.run(InterruptibleTask.java:57)
	at com.google.common.util.concurrent.TrustedListenableFutureTask.run(TrustedListenableFutureTask.java:78)
	at java.util.concurrent.ForkJoinTask$RunnableExecuteAction.exec(ForkJoinTask.java:1402)
	at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
	at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056)
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)

[Nov 6, 2018 13:30:02 ERROR TrackView] Failed to preprocess track GSM2692194_200#50615
Caused by: ERROR ClosedByInterruptException
java.nio.channels.ClosedByInterruptException
	at java.nio.channels.spi.AbstractInterruptibleChannel.end(AbstractInterruptibleChannel.java:202)
	at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:164)
	at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:65)
	at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:109)
	at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:103)
	at java.io.BufferedInputStream.read1(BufferedInputStream.java:284)
	at java.io.BufferedInputStream.read(BufferedInputStream.java:345)
	at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284)
	at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326)
	at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178)
	at java.io.InputStreamReader.read(InputStreamReader.java:184)
	at java.io.BufferedReader.fill(BufferedReader.java:161)
	at java.io.BufferedReader.read1(BufferedReader.java:212)
	at java.io.BufferedReader.read(BufferedReader.java:286)
	at com.google.gson.stream.JsonReader.fillBuffer(JsonReader.java:1287)
	at com.google.gson.stream.JsonReader.nextNonWhitespace(JsonReader.java:1325)
	at com.google.gson.stream.JsonReader.consumeNonExecutePrefix(JsonReader.java:1567)
	at com.google.gson.stream.JsonReader.doPeek(JsonReader.java:534)
	at com.google.gson.stream.JsonReader.peek(JsonReader.java:425)
	at com.google.gson.Gson.fromJson(Gson.java:883)
	at com.google.gson.Gson.fromJson(Gson.java:825)
	at org.jetbrains.bio.experiments.fit.SpanFitInformation$Companion.load(SpanModelFitExperiment.kt:141)
	at org.jetbrains.bio.experiments.fit.SpanModelFitExperiment$Companion.loadResults(SpanModelFitExperiment.kt:326)
	at org.jetbrains.bio.browser.span.SpanModelTrackView.preprocessImpl(SpanModelTrackView.kt:73)
	at org.jetbrains.bio.browser.tracks.TrackView.preprocess(TrackView.kt:173)
	at org.jetbrains.bio.browser.GenomeBrowser$preprocess$asTasks$1$$special$$inlined$map$lambda$1.call(GenomeBrowser.kt:286)
	at org.jetbrains.bio.browser.GenomeBrowser$preprocess$asTasks$1$$special$$inlined$map$lambda$1.call(GenomeBrowser.kt:28)
	at com.google.common.util.concurrent.TrustedListenableFutureTask$TrustedFutureInterruptibleTask.runInterruptibly(TrustedListenableFutureTask.java:125)
	at com.google.common.util.concurrent.InterruptibleTask.run(InterruptibleTask.java:57)
	at com.google.common.util.concurrent.TrustedListenableFutureTask.run(TrustedListenableFutureTask.java:78)
	at java.util.concurrent.ForkJoinTask$RunnableExecuteAction.exec(ForkJoinTask.java:1402)
	at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
	at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056)
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)

[Nov 6, 2018 13:30:02] Preprocess track 'GSM2692193_200#2ae6d': done in 33.54 s
[Nov 6, 2018 13:30:02] Preprocess track 'GSM2692194_200#50615': done in 33.54 s
[Nov 6, 2018 13:30:02] Preprocess: 13% (23/180), Elapsed time: 6 min, Throughput: 3 items/min, ETA: 41 min 2 s
@olegs
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olegs commented Nov 6, 2018

The same with opening lots of BED files:

[Nov 6, 2018 13:41:44] Processed 41,555 BED entries from /mnt/stripe/bio/raw-data/geo-samples/PRJNA392905/fastq_bams_span/GSM2692300_Spleen_B_Cell_ATAC_seq_mm10_0.01_5_peaks.bed
[Nov 6, 2018 13:41:48] Preprocess track 'GSM2692300_Spleen_B_Cell_ATAC_seq_mm10_0.01_5_peaks.bed': done in 2.909 min
[Nov 6, 2018 13:41:48] Preprocess track 'GSM2692309_Lung_Macrophage_ATAC_seq_mm10_0.01_5_peaks.bed'...
[Nov 6, 2018 13:41:48] Loading [3,4 mb] file: /mnt/stripe/bio/raw-data/geo-samples/PRJNA392905/fastq_bams_span/GSM2692309_Lung_Macrophage_ATAC_seq_mm10_0.01_5_peaks.bed
[Nov 6, 2018 13:41:48] Bed AUTO format: /mnt/stripe/bio/raw-data/geo-samples/PRJNA392905/fastq_bams_span/GSM2692309_Lung_Macrophage_ATAC_seq_mm10_0.01_5_peaks.bed = (bed6+3, '	')
[Nov 6, 2018 13:44:57] Processed 98,908 BED entries from /mnt/stripe/bio/raw-data/geo-samples/PRJNA392905/fastq_bams_span/GSM2692296_Skin_draining_lymph_node_Stromal_Cell_ATAC_seq_mm10_0.01_5_peaks.bed
[Nov 6, 2018 13:45:23] Preprocess track 'GSM2692310_Small_intestine_lamina_propria_Macrophage_ATAC_seq_mm10_0.01_5_peaks.bed'...
Exception in thread "Thread-31" java.lang.OutOfMemoryError: GC overhead limit exceeded
	at java.util.ArrayList.<init>(ArrayList.java:153)
	at kotlin.text.StringsKt__StringsKt.split$StringsKt__StringsKt(Strings.kt:1223)
	at kotlin.text.StringsKt__StringsKt.split(Strings.kt:1199)
	at kotlin.text.StringsKt__StringsKt.split$default(Strings.kt:1197)
	at org.jetbrains.bio.big.BedEntry.unpack(Bed.kt:73)
	at org.jetbrains.bio.big.BedEntry.unpack$default(Bed.kt:64)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$Companion$processBed$1$res$1.invoke(BedLocationTrackView.kt:274)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$Companion$processBed$1$res$1.invoke(BedLocationTrackView.kt:222)
	at kotlin.sequences.TransformingIndexedSequence$iterator$1.next(Sequences.kt:173)
	at kotlin.sequences.FilteringSequence$iterator$1.calcNext(Sequences.kt:109)
	at kotlin.sequences.FilteringSequence$iterator$1.hasNext(Sequences.kt:133)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$preprocessImpl$1.invoke(BedLocationTrackView.kt:326)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$preprocessImpl$1.invoke(BedLocationTrackView.kt:41)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$Companion$processBed$1.invoke(BedLocationTrackView.kt:280)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$Companion$processBed$1.invoke(BedLocationTrackView.kt:222)
	at org.jetbrains.bio.io.BedFormat.parse(Bed.kt:82)
	at org.jetbrains.bio.io.BedFormat.parse(Bed.kt:64)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$Companion.processBed(BedLocationTrackView.kt:268)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView.preprocessImpl(BedLocationTrackView.kt:99)
	at org.jetbrains.bio.browser.tracks.TrackView.preprocess(TrackView.kt:173)
	at org.jetbrains.bio.browser.GenomeBrowser$preprocess$asTasks$1$$special$$inlined$map$lambda$1.call(GenomeBrowser.kt:286)
	at org.jetbrains.bio.browser.GenomeBrowser$preprocess$asTasks$1$$special$$inlined$map$lambda$1.call(GenomeBrowser.kt:28)
	at com.google.common.util.concurrent.TrustedListenableFutureTask$TrustedFutureInterruptibleTask.runInterruptibly(TrustedListenableFutureTask.java:125)
	at com.google.common.util.concurrent.InterruptibleTask.run(InterruptibleTask.java:57)
	at com.google.common.util.concurrent.TrustedListenableFutureTask.run(TrustedListenableFutureTask.java:78)
	at java.util.concurrent.ForkJoinTask$RunnableExecuteAction.exec(ForkJoinTask.java:1402)
	at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
	at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056)
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)
[Nov 6, 2018 13:45:28 ERROR TrackView] Failed to preprocess track GSM2692305_Peritoneal_cavity_B_Cell_ATAC_seq_mm10_0.01_5_peaks.bed
Caused by: ERROR ClosedByInterruptException
java.nio.channels.ClosedByInterruptException
	at java.nio.channels.spi.AbstractInterruptibleChannel.end(AbstractInterruptibleChannel.java:202)
	at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:164)
	at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:65)
	at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:109)
	at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:103)
	at java.io.BufferedInputStream.read1(BufferedInputStream.java:284)
	at java.io.BufferedInputStream.read(BufferedInputStream.java:345)
	at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284)
	at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326)
	at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178)
	at java.io.InputStreamReader.read(InputStreamReader.java:184)
	at java.io.BufferedReader.fill(BufferedReader.java:161)
	at java.io.BufferedReader.readLine(BufferedReader.java:324)
	at java.io.BufferedReader.readLine(BufferedReader.java:389)
	at org.jetbrains.bio.io.BedParser.readLine(Bed.kt:300)
	at org.jetbrains.bio.io.BedParser.access$readLine(Bed.kt:275)
	at org.jetbrains.bio.io.BedParser$iterator$1.next(Bed.kt:288)
	at org.jetbrains.bio.io.BedParser$iterator$1.next(Bed.kt:283)
	at kotlin.sequences.TransformingIndexedSequence$iterator$1.next(Sequences.kt:173)
	at kotlin.sequences.FilteringSequence$iterator$1.calcNext(Sequences.kt:109)
	at kotlin.sequences.FilteringSequence$iterator$1.hasNext(Sequences.kt:133)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$preprocessImpl$1.invoke(BedLocationTrackView.kt:326)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$preprocessImpl$1.invoke(BedLocationTrackView.kt:41)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$Companion$processBed$1.invoke(BedLocationTrackView.kt:280)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$Companion$processBed$1.invoke(BedLocationTrackView.kt:222)
	at org.jetbrains.bio.io.BedFormat.parse(Bed.kt:82)
	at org.jetbrains.bio.io.BedFormat.parse(Bed.kt:64)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$Companion.processBed(BedLocationTrackView.kt:268)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView.preprocessImpl(BedLocationTrackView.kt:99)
	at org.jetbrains.bio.browser.tracks.TrackView.preprocess(TrackView.kt:173)
	at org.jetbrains.bio.browser.GenomeBrowser$preprocess$asTasks$1$$special$$inlined$map$lambda$1.call(GenomeBrowser.kt:286)
	at org.jetbrains.bio.browser.GenomeBrowser$preprocess$asTasks$1$$special$$inlined$map$lambda$1.call(GenomeBrowser.kt:28)
	at com.google.common.util.concurrent.TrustedListenableFutureTask$TrustedFutureInterruptibleTask.runInterruptibly(TrustedListenableFutureTask.java:125)
	at com.google.common.util.concurrent.InterruptibleTask.run(InterruptibleTask.java:57)
	at com.google.common.util.concurrent.TrustedListenableFutureTask.run(TrustedListenableFutureTask.java:78)
	at java.util.concurrent.ForkJoinTask$RunnableExecuteAction.exec(ForkJoinTask.java:1402)
	at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
	at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056)
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)

[Nov 6, 2018 13:45:28] Loading [3,5 mb] file: /mnt/stripe/bio/raw-data/geo-samples/PRJNA392905/fastq_bams_span/GSM2692310_Small_intestine_lamina_propria_Macrophage_ATAC_seq_mm10_0.01_5_peaks.bed
[Nov 6, 2018 13:45:28] Preprocess track 'GSM2692305_Peritoneal_cavity_B_Cell_ATAC_seq_mm10_0.01_5_peaks.bed': done in 4.586 min
[Nov 6, 2018 13:45:28 ERROR TrackView] Failed to preprocess track GSM2692280_Blood_Monocyte_ATAC_seq_mm10_0.01_5_peaks.bed
Caused by: ERROR ClosedByInterruptException
java.nio.channels.ClosedByInterruptException
	at java.nio.channels.spi.AbstractInterruptibleChannel.end(AbstractInterruptibleChannel.java:202)
	at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:164)
	at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:65)
	at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:109)
	at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:103)
	at java.io.BufferedInputStream.read1(BufferedInputStream.java:284)
	at java.io.BufferedInputStream.read(BufferedInputStream.java:345)
	at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284)
	at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326)
	at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178)
	at java.io.InputStreamReader.read(InputStreamReader.java:184)
	at java.io.BufferedReader.fill(BufferedReader.java:161)
	at java.io.BufferedReader.readLine(BufferedReader.java:324)
	at java.io.BufferedReader.readLine(BufferedReader.java:389)
	at org.jetbrains.bio.io.BedParser.readLine(Bed.kt:300)
	at org.jetbrains.bio.io.BedParser.access$readLine(Bed.kt:275)
	at org.jetbrains.bio.io.BedParser$iterator$1.next(Bed.kt:288)
	at org.jetbrains.bio.io.BedParser$iterator$1.next(Bed.kt:283)
	at kotlin.sequences.TransformingIndexedSequence$iterator$1.next(Sequences.kt:173)
	at kotlin.sequences.FilteringSequence$iterator$1.calcNext(Sequences.kt:109)
	at kotlin.sequences.FilteringSequence$iterator$1.hasNext(Sequences.kt:133)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$preprocessImpl$1.invoke(BedLocationTrackView.kt:326)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$preprocessImpl$1.invoke(BedLocationTrackView.kt:41)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$Companion$processBed$1.invoke(BedLocationTrackView.kt:280)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$Companion$processBed$1.invoke(BedLocationTrackView.kt:222)
	at org.jetbrains.bio.io.BedFormat.parse(Bed.kt:82)
	at org.jetbrains.bio.io.BedFormat.parse(Bed.kt:64)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$Companion.processBed(BedLocationTrackView.kt:268)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView.preprocessImpl(BedLocationTrackView.kt:99)
	at org.jetbrains.bio.browser.tracks.TrackView.preprocess(TrackView.kt:173)
	at org.jetbrains.bio.browser.GenomeBrowser$preprocess$asTasks$1$$special$$inlined$map$lambda$1.call(GenomeBrowser.kt:286)
	at org.jetbrains.bio.browser.GenomeBrowser$preprocess$asTasks$1$$special$$inlined$map$lambda$1.call(GenomeBrowser.kt:28)
	at com.google.common.util.concurrent.TrustedListenableFutureTask$TrustedFutureInterruptibleTask.runInterruptibly(TrustedListenableFutureTask.java:125)
	at com.google.common.util.concurrent.InterruptibleTask.run(InterruptibleTask.java:57)
	at com.google.common.util.concurrent.TrustedListenableFutureTask.run(TrustedListenableFutureTask.java:78)
	at java.util.concurrent.ForkJoinTask$RunnableExecuteAction.exec(ForkJoinTask.java:1402)
	at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
	at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056)
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)

[Nov 6, 2018 13:45:28 ERROR TrackView] Failed to preprocess track GSM2692308_Lung_Macrophage_ATAC_seq_mm10_0.01_5_peaks.bed
Caused by: ERROR ClosedByInterruptException
java.nio.channels.ClosedByInterruptException
	at java.nio.channels.spi.AbstractInterruptibleChannel.end(AbstractInterruptibleChannel.java:202)
	at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:164)
	at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:65)
	at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:109)
	at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:103)
	at java.io.BufferedInputStream.read1(BufferedInputStream.java:284)
	at java.io.BufferedInputStream.read(BufferedInputStream.java:345)
	at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284)
	at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326)
	at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178)
	at java.io.InputStreamReader.read(InputStreamReader.java:184)
	at java.io.BufferedReader.fill(BufferedReader.java:161)
	at java.io.BufferedReader.readLine(BufferedReader.java:324)
	at java.io.BufferedReader.readLine(BufferedReader.java:389)
	at org.jetbrains.bio.io.BedParser.readLine(Bed.kt:300)
	at org.jetbrains.bio.io.BedParser.access$readLine(Bed.kt:275)
	at org.jetbrains.bio.io.BedParser$iterator$1.next(Bed.kt:288)
	at org.jetbrains.bio.io.BedParser$iterator$1.next(Bed.kt:283)
	at kotlin.sequences.TransformingIndexedSequence$iterator$1.next(Sequences.kt:173)
	at kotlin.sequences.FilteringSequence$iterator$1.calcNext(Sequences.kt:109)
	at kotlin.sequences.FilteringSequence$iterator$1.hasNext(Sequences.kt:133)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$preprocessImpl$1.invoke(BedLocationTrackView.kt:326)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$preprocessImpl$1.invoke(BedLocationTrackView.kt:41)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$Companion$processBed$1.invoke(BedLocationTrackView.kt:280)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$Companion$processBed$1.invoke(BedLocationTrackView.kt:222)
	at org.jetbrains.bio.io.BedFormat.parse(Bed.kt:82)
	at org.jetbrains.bio.io.BedFormat.parse(Bed.kt:64)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$Companion.processBed(BedLocationTrackView.kt:268)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView.preprocessImpl(BedLocationTrackView.kt:99)
	at org.jetbrains.bio.browser.tracks.TrackView.preprocess(TrackView.kt:173)
	at org.jetbrains.bio.browser.GenomeBrowser$preprocess$asTasks$1$$special$$inlined$map$lambda$1.call(GenomeBrowser.kt:286)
	at org.jetbrains.bio.browser.GenomeBrowser$preprocess$asTasks$1$$special$$inlined$map$lambda$1.call(GenomeBrowser.kt:28)
	at com.google.common.util.concurrent.TrustedListenableFutureTask$TrustedFutureInterruptibleTask.runInterruptibly(TrustedListenableFutureTask.java:125)
	at com.google.common.util.concurrent.InterruptibleTask.run(InterruptibleTask.java:57)
	at com.google.common.util.concurrent.TrustedListenableFutureTask.run(TrustedListenableFutureTask.java:78)
	at java.util.concurrent.ForkJoinTask$RunnableExecuteAction.exec(ForkJoinTask.java:1402)
	at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
	at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056)
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)

[Nov 6, 2018 13:45:28 ERROR TrackView] Failed to preprocess track GSM2692307_Lung_Macrophage_ATAC_seq_mm10_0.01_5_peaks.bed
Caused by: ERROR ClosedByInterruptException
java.nio.channels.ClosedByInterruptException
	at java.nio.channels.spi.AbstractInterruptibleChannel.end(AbstractInterruptibleChannel.java:202)
	at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:164)
	at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:65)
	at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:109)
	at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:103)
	at java.io.BufferedInputStream.read1(BufferedInputStream.java:284)
	at java.io.BufferedInputStream.read(BufferedInputStream.java:345)
	at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284)
	at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326)
	at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178)
	at java.io.InputStreamReader.read(InputStreamReader.java:184)
	at java.io.BufferedReader.fill(BufferedReader.java:161)
	at java.io.BufferedReader.readLine(BufferedReader.java:324)
	at java.io.BufferedReader.readLine(BufferedReader.java:389)
	at org.jetbrains.bio.io.BedParser.readLine(Bed.kt:300)
	at org.jetbrains.bio.io.BedParser.access$readLine(Bed.kt:275)
	at org.jetbrains.bio.io.BedParser$iterator$1.next(Bed.kt:288)
	at org.jetbrains.bio.io.BedParser$iterator$1.next(Bed.kt:283)
	at kotlin.sequences.TransformingIndexedSequence$iterator$1.next(Sequences.kt:173)
	at kotlin.sequences.FilteringSequence$iterator$1.calcNext(Sequences.kt:109)
	at kotlin.sequences.FilteringSequence$iterator$1.hasNext(Sequences.kt:133)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$preprocessImpl$1.invoke(BedLocationTrackView.kt:326)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$preprocessImpl$1.invoke(BedLocationTrackView.kt:41)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$Companion$processBed$1.invoke(BedLocationTrackView.kt:280)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$Companion$processBed$1.invoke(BedLocationTrackView.kt:222)
	at org.jetbrains.bio.io.BedFormat.parse(Bed.kt:82)
	at org.jetbrains.bio.io.BedFormat.parse(Bed.kt:64)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$Companion.processBed(BedLocationTrackView.kt:268)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView.preprocessImpl(BedLocationTrackView.kt:99)
	at org.jetbrains.bio.browser.tracks.TrackView.preprocess(TrackView.kt:173)
	at org.jetbrains.bio.browser.GenomeBrowser$preprocess$asTasks$1$$special$$inlined$map$lambda$1.call(GenomeBrowser.kt:286)
	at org.jetbrains.bio.browser.GenomeBrowser$preprocess$asTasks$1$$special$$inlined$map$lambda$1.call(GenomeBrowser.kt:28)
	at com.google.common.util.concurrent.TrustedListenableFutureTask$TrustedFutureInterruptibleTask.runInterruptibly(TrustedListenableFutureTask.java:125)
	at com.google.common.util.concurrent.InterruptibleTask.run(InterruptibleTask.java:57)
	at com.google.common.util.concurrent.TrustedListenableFutureTask.run(TrustedListenableFutureTask.java:78)
	at java.util.concurrent.ForkJoinTask$RunnableExecuteAction.exec(ForkJoinTask.java:1402)
	at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
	at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056)
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)

[Nov 6, 2018 13:45:28] Preprocess track 'GSM2692307_Lung_Macrophage_ATAC_seq_mm10_0.01_5_peaks.bed': done in 4.190 min
[Nov 6, 2018 13:45:28 ERROR TrackView] Failed to preprocess track GSM2692306_Lung_Macrophage_ATAC_seq_mm10_0.01_5_peaks.bed
Caused by: ERROR ClosedByInterruptException
java.nio.channels.ClosedByInterruptException
	at java.nio.channels.spi.AbstractInterruptibleChannel.end(AbstractInterruptibleChannel.java:202)
	at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:164)
	at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:65)
	at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:109)
	at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:103)
	at java.io.BufferedInputStream.read1(BufferedInputStream.java:284)
	at java.io.BufferedInputStream.read(BufferedInputStream.java:345)
	at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284)
	at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326)
	at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178)
	at java.io.InputStreamReader.read(InputStreamReader.java:184)
	at java.io.BufferedReader.fill(BufferedReader.java:161)
	at java.io.BufferedReader.readLine(BufferedReader.java:324)
	at java.io.BufferedReader.readLine(BufferedReader.java:389)
	at org.jetbrains.bio.io.BedParser.readLine(Bed.kt:300)
	at org.jetbrains.bio.io.BedParser.access$readLine(Bed.kt:275)
	at org.jetbrains.bio.io.BedParser$iterator$1.next(Bed.kt:288)
	at org.jetbrains.bio.io.BedParser$iterator$1.next(Bed.kt:283)
	at kotlin.sequences.TransformingIndexedSequence$iterator$1.next(Sequences.kt:173)
	at kotlin.sequences.FilteringSequence$iterator$1.calcNext(Sequences.kt:109)
	at kotlin.sequences.FilteringSequence$iterator$1.hasNext(Sequences.kt:133)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$preprocessImpl$1.invoke(BedLocationTrackView.kt:326)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$preprocessImpl$1.invoke(BedLocationTrackView.kt:41)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$Companion$processBed$1.invoke(BedLocationTrackView.kt:280)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$Companion$processBed$1.invoke(BedLocationTrackView.kt:222)
	at org.jetbrains.bio.io.BedFormat.parse(Bed.kt:82)
	at org.jetbrains.bio.io.BedFormat.parse(Bed.kt:64)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$Companion.processBed(BedLocationTrackView.kt:268)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView.preprocessImpl(BedLocationTrackView.kt:99)
	at org.jetbrains.bio.browser.tracks.TrackView.preprocess(TrackView.kt:173)
	at org.jetbrains.bio.browser.GenomeBrowser$preprocess$asTasks$1$$special$$inlined$map$lambda$1.call(GenomeBrowser.kt:286)
	at org.jetbrains.bio.browser.GenomeBrowser$preprocess$asTasks$1$$special$$inlined$map$lambda$1.call(GenomeBrowser.kt:28)
	at com.google.common.util.concurrent.TrustedListenableFutureTask$TrustedFutureInterruptibleTask.runInterruptibly(TrustedListenableFutureTask.java:125)
	at com.google.common.util.concurrent.InterruptibleTask.run(InterruptibleTask.java:57)
	at com.google.common.util.concurrent.TrustedListenableFutureTask.run(TrustedListenableFutureTask.java:78)
	at java.util.concurrent.ForkJoinTask$RunnableExecuteAction.exec(ForkJoinTask.java:1402)
	at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
	at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056)
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)

[Nov 6, 2018 13:45:28] Preprocess track 'GSM2692306_Lung_Macrophage_ATAC_seq_mm10_0.01_5_peaks.bed': done in 4.330 min
[Nov 6, 2018 13:45:28 ERROR TrackView] Failed to preprocess track GSM2692309_Lung_Macrophage_ATAC_seq_mm10_0.01_5_peaks.bed
Caused by: ERROR ClosedByInterruptException
java.nio.channels.ClosedByInterruptException
	at java.nio.channels.spi.AbstractInterruptibleChannel.end(AbstractInterruptibleChannel.java:202)
	at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:164)
	at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:65)
	at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:109)
	at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:103)
	at java.io.BufferedInputStream.read1(BufferedInputStream.java:284)
	at java.io.BufferedInputStream.read(BufferedInputStream.java:345)
	at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284)
	at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326)
	at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178)
	at java.io.InputStreamReader.read(InputStreamReader.java:184)
	at java.io.BufferedReader.fill(BufferedReader.java:161)
	at java.io.BufferedReader.readLine(BufferedReader.java:324)
	at java.io.BufferedReader.readLine(BufferedReader.java:389)
	at org.jetbrains.bio.io.BedParser.readLine(Bed.kt:300)
	at org.jetbrains.bio.io.BedParser.access$readLine(Bed.kt:275)
	at org.jetbrains.bio.io.BedParser$iterator$1.next(Bed.kt:288)
	at org.jetbrains.bio.io.BedParser$iterator$1.next(Bed.kt:283)
	at kotlin.sequences.TransformingIndexedSequence$iterator$1.next(Sequences.kt:173)
	at kotlin.sequences.FilteringSequence$iterator$1.calcNext(Sequences.kt:109)
	at kotlin.sequences.FilteringSequence$iterator$1.hasNext(Sequences.kt:133)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$preprocessImpl$1.invoke(BedLocationTrackView.kt:326)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$preprocessImpl$1.invoke(BedLocationTrackView.kt:41)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$Companion$processBed$1.invoke(BedLocationTrackView.kt:280)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$Companion$processBed$1.invoke(BedLocationTrackView.kt:222)
	at org.jetbrains.bio.io.BedFormat.parse(Bed.kt:82)
	at org.jetbrains.bio.io.BedFormat.parse(Bed.kt:64)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$Companion.processBed(BedLocationTrackView.kt:268)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView.preprocessImpl(BedLocationTrackView.kt:99)
	at org.jetbrains.bio.browser.tracks.TrackView.preprocess(TrackView.kt:173)
	at org.jetbrains.bio.browser.GenomeBrowser$preprocess$asTasks$1$$special$$inlined$map$lambda$1.call(GenomeBrowser.kt:286)
	at org.jetbrains.bio.browser.GenomeBrowser$preprocess$asTasks$1$$special$$inlined$map$lambda$1.call(GenomeBrowser.kt:28)
	at com.google.common.util.concurrent.TrustedListenableFutureTask$TrustedFutureInterruptibleTask.runInterruptibly(TrustedListenableFutureTask.java:125)
	at com.google.common.util.concurrent.InterruptibleTask.run(InterruptibleTask.java:57)
	at com.google.common.util.concurrent.TrustedListenableFutureTask.run(TrustedListenableFutureTask.java:78)
	at java.util.concurrent.ForkJoinTask$RunnableExecuteAction.exec(ForkJoinTask.java:1402)
	at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
	at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056)
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)

[Nov 6, 2018 13:45:31] Preprocess track 'GSM2692309_Lung_Macrophage_ATAC_seq_mm10_0.01_5_peaks.bed': done in 3.718 min
[Nov 6, 2018 13:45:31 ERROR TrackView] Failed to preprocess track GSM2692310_Small_intestine_lamina_propria_Macrophage_ATAC_seq_mm10_0.01_5_peaks.bed
Caused by: ERROR ClosedByInterruptException
java.nio.channels.ClosedByInterruptException
	at java.nio.channels.spi.AbstractInterruptibleChannel.end(AbstractInterruptibleChannel.java:202)
	at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:164)
	at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:65)
	at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:109)
	at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:103)
	at java.io.BufferedInputStream.read1(BufferedInputStream.java:284)
	at java.io.BufferedInputStream.read(BufferedInputStream.java:345)
	at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284)
	at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326)
	at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178)
	at java.io.InputStreamReader.read(InputStreamReader.java:184)
	at java.io.BufferedReader.fill(BufferedReader.java:161)
	at java.io.BufferedReader.readLine(BufferedReader.java:324)
	at java.io.BufferedReader.readLine(BufferedReader.java:389)
	at org.jetbrains.bio.io.BedFormat$Companion.detectDelimiter(Bed.kt:153)
	at org.jetbrains.bio.io.BedFormat$Companion.auto(Bed.kt:191)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView$Companion.processBed(BedLocationTrackView.kt:262)
	at org.jetbrains.bio.browser.tracks.impl.BedLocationTrackView.preprocessImpl(BedLocationTrackView.kt:99)
	at org.jetbrains.bio.browser.tracks.TrackView.preprocess(TrackView.kt:173)
	at org.jetbrains.bio.browser.GenomeBrowser$preprocess$asTasks$1$$special$$inlined$map$lambda$1.call(GenomeBrowser.kt:286)
	at org.jetbrains.bio.browser.GenomeBrowser$preprocess$asTasks$1$$special$$inlined$map$lambda$1.call(GenomeBrowser.kt:28)
	at com.google.common.util.concurrent.TrustedListenableFutureTask$TrustedFutureInterruptibleTask.runInterruptibly(TrustedListenableFutureTask.java:125)
	at com.google.common.util.concurrent.InterruptibleTask.run(InterruptibleTask.java:57)
	at com.google.common.util.concurrent.TrustedListenableFutureTask.run(TrustedListenableFutureTask.java:78)
	at java.util.concurrent.ForkJoinTask$RunnableExecuteAction.exec(ForkJoinTask.java:1402)
	at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
	at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056)
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)

[Nov 6, 2018 13:45:31] Preprocess track 'GSM2692308_Lung_Macrophage_ATAC_seq_mm10_0.01_5_peaks.bed': done in 3.914 min
[Nov 6, 2018 13:45:31] Preprocess track 'GSM2692310_Small_intestine_lamina_propria_Macrophage_ATAC_seq_mm10_0.01_5_peaks.bed': done in 8.445 s
[Nov 6, 2018 13:45:31] Preprocess track 'GSM2692280_Blood_Monocyte_ATAC_seq_mm10_0.01_5_peaks.bed': done in 9.713 min
[Nov 6, 2018 13:45:31] Preprocess: 74% (134/180), Elapsed time: 11 min 9 s, Throughput: 4 s/item, ETA: 3 min 49 s
[Nov 6, 2018 13:45:31] Preprocess track 'GSM2692296_Skin_draining_lymph_node_Stromal_Cell_ATAC_seq_mm10_0.01_5_peaks.bed': done in 7.537 min

@dievsky
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dievsky commented Nov 6, 2018

I can confirm that this can (and does) happen.
That's likely caused by the fact that we catch Exceptions in TrackView.preprocess, but not Errors.

@olegs
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olegs commented Nov 6, 2018

Since JBR remains fully functional after this happens, we should try to show some feedback to user except errors in logs.

@dievsky
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dievsky commented Nov 6, 2018

@olegs I agree fully. We can try to catch the OOM and report it as a processing error.

@iromeo
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iromeo commented Nov 6, 2018

TODO:

  • Is 2GB xmx enough or better to used 3-4 GB ?
  • In case of OOM errors show IDEA-like corresponding error message + allow to change XMX because it isn't a trivial task for a user
  • In case of OOM while rendering (not only preprocess) consider some action, e.g. set OOM error to track's preprocessing error

@dievsky
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dievsky commented Nov 6, 2018

In case of OOM while rendering (not only preprocess) consider some action, e.g. set OOM error to track's preprocessing error

There's a problem here: memory isn't freed in this scenario, so now the browser and its components won't have enough memory to function normally. We could instruct the track to release its data or replace the failed track with a dummy one.

@olegs olegs transferred this issue from another repository Mar 24, 2019
@iromeo iromeo assigned PetrTsurinov and unassigned iromeo Mar 28, 2019
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