search

JetBrains-Research / jbr

JBR Genome Browser
https://doi.org/10.1093/bioinformatics/btab376
11 stars 0 forks source link

ERROR during adding large BED file in JBR #176

Closed olegs closed 2 years ago

olegs commented 2 years ago 
[Jul 28, 2022 22:55:29] ERROR TrackViewLoader Cannot load Track file:/Users/Oleg.Shpynov/data/2022_GSE26320/hg38_dhs_ENCFF304XEX.bed
Caused by: ERROR TribbleException$MalformedFeatureFile Input file is not sorted by start position. 
We saw a record with a start of chr1:121275232 after a record with a start of chr1:121275589, for input source: /Users/Oleg.Shpynov/data/2022_GSE26320/hg38_dhs_ENCFF304XEX.bed
htsjdk.tribble.index.IndexFactory.checkSorted(IndexFactory.java:413)
htsjdk.tribble.index.IndexFactory.createIndex(IndexFactory.java:377)
htsjdk.tribble.index.IndexFactory.createLinearIndex(IndexFactory.java:242)
htsjdk.tribble.index.IndexFactory.createLinearIndex(IndexFactory.java:228)
org.jetbrains.bio.browser.tracks.bed.IndexedBedTrackView$Companion.create(IndexedBedTrackView.kt:233)
org.jetbrains.bio.browser.tracks.bed.IndexedBedTrackView$Companion.create$default(IndexedBedTrackView.kt:212)
org.jetbrains.bio.browser.file.PeaksTrackViewExtensionPoint$Companion$BED_LOCATIONS$1.createTrackViewImpl(TrackViewTypeExtensionPoints.kt:114)
org.jetbrains.bio.browser.file.PeaksTrackViewExtensionPoint$Companion$BED_LOCATIONS$1.createTrackViewImpl(TrackViewTypeExtensionPoints.kt:106)
org.jetbrains.bio.browser.file.TrackViewType.createTrackView(TrackViewType.kt:50)
org.jetbrains.bio.browser.file.TrackViewLoader.createTrackViews(TrackViewLoader.kt:55)
org.jetbrains.bio.browser.desktop.TrackListController$createAndAddTrackViews$2.invoke(TrackListController.kt:312)
org.jetbrains.bio.browser.desktop.TrackListController$createAndAddTrackViews$2.invoke(TrackListController.kt:311)
org.jetbrains.bio.browser.desktop.DesktopGenomeBrowser$addAndProcessNewTracks$1.invoke(DesktopGenomeBrowser.kt:342)
org.jetbrains.bio.browser.desktop.DesktopGenomeBrowser$addAndProcessNewTracks$1.invoke(DesktopGenomeBrowser.kt:340)
org.jetbrains.bio.browser.desktop.dialogs.ProgressDialog$display$block$1.invoke$lambda-1(ProgressDialog.kt:173)
java.base/java.lang.Thread.run(Thread.java:833)
[Jul 28, 2022 22:55:29] 'Loading files': Preprocessing 0 tracks
[Jul 28, 2022 22:55:29] Preprocessing: 100%, Elapsed time: 34 μs [done]
[Jul 28, 2022 22:55:29] TRACE GroupScales Initializing group scales
[Jul 28, 2022 22:55:29] DEBUG ProgressDialog Detach progress log appender
[Jul 28, 2022 22:56:29] DEBUG ProgressDialog Init progress log appender
[Jul 28, 2022 22:56:29] [1/1] Loading file:/Users/Oleg.Shpynov/data/2022_GSE26320/hg38_dhs_ENCFF304XEX_sorted.bed as BED_LOCATIONS
...
olegs commented 2 years ago

The problem is that file is not sorted, error shown.