[IGBF-2954] Investigate: why is loading bb (bigbed) and bigwig (bw) files so slow? - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: None
Labels:
None

Story Points:
1.5
Epic Link:
Improve IGB for users
Sprint:
Fall 4 2021 Sep 27 - Oct 8, Fall 5 2021 Oct 11 - Oct 22

Description

See linked issue for track hub facade data sources URL for the "JASPAR" Track Hub with multiple bigbed files.

Loading these data into IGB is extremely slow for some reason.

Bigbed format files contain indexes that map chromosome positions onto file byte positions, which let client software programs (like IGB) look up exactly which part of the larger file they need and then use HTTP byte range requests to retrieve just the needed portion of the file. Therefore it is surprising that loading this file takes a long time with IGB. Retrieving and reading the index part of the file should be very fast, and requesting the bytes ought to be fast, as well.

For this task, investigate why it is so slow and suggest some ideas for how to speed it up.

The bb (bigbed) format is commonly used in bioinformatics for distributing and visualizing data, so it is important that we do a better job of supporting it.

Attachments

Issue Links

relates to

IGBF-2948 Attempt to convert and load each track hub featured in the table interface

Closed

IGBF-1938 Investigate: Why is bigwig loading so slow?

To-Do

IGBF-2979 Investigate: bigBed chromosome synonyms logic

To-Do

IGBF-2944 Update annots.xml url validation and filetype determination for trackhubs

Closed

IGBF-2978 Improve bigBed parsing

Closed

IGBF-1417 Create new artifact with bigbed and bigwig parsing code from IGV codebase

Closed

IGBF-2911 Handle araTha1 synonym in track hub facade

Closed

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Ann Loraine added a comment - 22/Sep/21 5:17 PM

Downloaded the slow-loading bb file:

wget http://expdata.cmmt.ubc.ca/JASPAR/downloads/UCSC_tracks/2022/JASPAR2022_araTha1.bb

The file is more than 2 Gb in size.

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Ann Loraine added a comment - 22/Sep/21 5:17 PM Downloaded the slow-loading bb file: wget http: //expdata.cmmt.ubc.ca/JASPAR/downloads/UCSC_tracks/2022/JASPAR2022_araTha1.bb The file is more than 2 Gb in size.

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Ann Loraine added a comment - 28/Sep/21 10:13 AM - edited

Nowlan Freese notes that bigwig loading is also very slow while testing ~~IGBF-2911~~.

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Ann Loraine added a comment - 28/Sep/21 10:13 AM - edited Nowlan Freese notes that bigwig loading is also very slow while testing IGBF-2911 .

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Nowlan Freese added a comment - 29/Sep/21 4:39 PM - edited

Initial notes on loading bigwig files:

Testing using branch release-9.1.8 on Netbeans 8.2.

Attempting to load the file SRR10060893.rnaseq.bw locally works fine and is relatively fast. When I attempt to load the file from BioViz Connect it locks up IGB for several minutes.

The problem appears to be occurring within the following line of code from BBFileReader.java:

zoomLevels = new BBZoomLevels(fis, zoomLevelOffset, zoomLevelCount,
                    isLowToHigh, uncompressBufSize);

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Nowlan Freese added a comment - 29/Sep/21 4:39 PM - edited Initial notes on loading bigwig files: Testing using branch release-9.1.8 on Netbeans 8.2. Attempting to load the file SRR10060893.rnaseq.bw locally works fine and is relatively fast. When I attempt to load the file from BioViz Connect it locks up IGB for several minutes. The problem appears to be occurring within the following line of code from BBFileReader.java: zoomLevels = new BBZoomLevels(fis, zoomLevelOffset, zoomLevelCount, isLowToHigh, uncompressBufSize);

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Ann Loraine added a comment - 30/Sep/21 10:36 AM

Check for caching. If a file has to downloaded in its entirety in order to be displayed in IGB, the application may be saving it in the local cache.

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Ann Loraine added a comment - 30/Sep/21 10:36 AM Check for caching. If a file has to downloaded in its entirety in order to be displayed in IGB, the application may be saving it in the local cache.

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Nowlan Freese added a comment - 30/Sep/21 10:50 AM

Repository for bigwig and bigbed parsing: https://bitbucket.org/lorainelab/bigwig/src/master/

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Nowlan Freese added a comment - 30/Sep/21 10:50 AM Repository for bigwig and bigbed parsing: https://bitbucket.org/lorainelab/bigwig/src/master/

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Nowlan Freese added a comment - 30/Sep/21 2:40 PM

14:39:52.180 ERROR o.broad.igv.bbfile.BBZoomLevelFormat - Error reading zoom level data records (Table O)
java.io.EOFException: null
at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:86) ~[htsjdk-igb-2.16.3.jar:na]
at org.broad.igv.bbfile.BBZoomLevelFormat.<init>(BBZoomLevelFormat.java:113) ~[bigwig-2.0.0.jar:na]
at org.broad.igv.bbfile.BBZoomLevels.<init>(BBZoomLevels.java:115) [bigwig-2.0.0.jar:na]
at org.broad.igv.bbfile.BBFileReader.<init>(BBFileReader.java:166) [bigwig-2.0.0.jar:na]
at com.gene.bigwighandler.BigWigSymLoader.initbbReader(BigWigSymLoader.java:89) [bigWigHandler-9.1.10.jar:na]
at com.gene.bigwighandler.BigWigSymLoader.init(BigWigSymLoader.java:62) [bigWigHandler-9.1.10.jar:na]
at com.gene.bigwighandler.BigWigSymLoader.getChromosomeList(BigWigSymLoader.java:106) [bigWigHandler-9.1.10.jar:na]
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:153) [genometry-9.1.10.jar:na]
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:139) [genometry-9.1.10.jar:na]
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:119) [genometry-9.1.10.jar:na]
at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:752) [igb-9.1.10.jar:na]
at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:694) [igb-9.1.10.jar:na]
at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:689) [igb-9.1.10.jar:na]
at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73) [genometry-9.1.10.jar:na]
at javax.swing.SwingWorker$1.call(SwingWorker.java:295) [na:1.8.0_241]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_241]
at javax.swing.SwingWorker.run(SwingWorker.java:334) [na:1.8.0_241]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [na:1.8.0_241]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [na:1.8.0_241]
at java.lang.Thread.run(Thread.java:748) [na:1.8.0_241]

https://data.cyverse.org/dav-anon/iplant/home/shared/BioViz/rnaseq/A_thaliana_Jun_2009/SRP220157/graph_scaled/SRR10060904.rnaseq.bw

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Nowlan Freese added a comment - 30/Sep/21 2:40 PM 14:39:52.180 ERROR o.broad.igv.bbfile.BBZoomLevelFormat - Error reading zoom level data records (Table O) java.io.EOFException: null at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:86) ~ [htsjdk-igb-2.16.3.jar:na] at org.broad.igv.bbfile.BBZoomLevelFormat.<init>(BBZoomLevelFormat.java:113) ~ [bigwig-2.0.0.jar:na] at org.broad.igv.bbfile.BBZoomLevels.<init>(BBZoomLevels.java:115) [bigwig-2.0.0.jar:na] at org.broad.igv.bbfile.BBFileReader.<init>(BBFileReader.java:166) [bigwig-2.0.0.jar:na] at com.gene.bigwighandler.BigWigSymLoader.initbbReader(BigWigSymLoader.java:89) [bigWigHandler-9.1.10.jar:na] at com.gene.bigwighandler.BigWigSymLoader.init(BigWigSymLoader.java:62) [bigWigHandler-9.1.10.jar:na] at com.gene.bigwighandler.BigWigSymLoader.getChromosomeList(BigWigSymLoader.java:106) [bigWigHandler-9.1.10.jar:na] at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:153) [genometry-9.1.10.jar:na] at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:139) [genometry-9.1.10.jar:na] at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:119) [genometry-9.1.10.jar:na] at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:752) [igb-9.1.10.jar:na] at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:694) [igb-9.1.10.jar:na] at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:689) [igb-9.1.10.jar:na] at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73) [genometry-9.1.10.jar:na] at javax.swing.SwingWorker$1.call(SwingWorker.java:295) [na:1.8.0_241] at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_241] at javax.swing.SwingWorker.run(SwingWorker.java:334) [na:1.8.0_241] at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [na:1.8.0_241] at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [na:1.8.0_241] at java.lang.Thread.run(Thread.java:748) [na:1.8.0_241] https://data.cyverse.org/dav-anon/iplant/home/shared/BioViz/rnaseq/A_thaliana_Jun_2009/SRP220157/graph_scaled/SRR10060904.rnaseq.bw

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Nowlan Freese added a comment - 14/Oct/21 1:47 PM

Link to public Quickload hosted on CyVerse:

https://data.cyverse.org/dav-anon/iplant/home/nfreese/2954_testing/quickload

Contains a bigBed, bed and tabix indexed bed file created from Araport11 on IGB Quickload. Also contains bedgraph, bigwig, wig, and tabix indexed bedgraph of the SRR10060893 bedgraph file from the BioViz CyVerse community folder.

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Nowlan Freese added a comment - 14/Oct/21 1:47 PM Link to public Quickload hosted on CyVerse: https://data.cyverse.org/dav-anon/iplant/home/nfreese/2954_testing/quickload Contains a bigBed, bed and tabix indexed bed file created from Araport11 on IGB Quickload. Also contains bedgraph, bigwig, wig, and tabix indexed bedgraph of the SRR10060893 bedgraph file from the BioViz CyVerse community folder.

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Nowlan Freese added a comment - 14/Oct/21 2:26 PM - edited

Testing in 9.1.8 release

For files, use the above quickload hosted on CyVerse.
In IGB
Open the Arabidopsis thaliana genome A_thaliana_Jun_2009
Navigate to Chr1:2,257,247-2,260,234
Select bigBed, bed, bed tabix in the Available Data box

I see no difference in loading times, with or without the cache enabled. I also don't see anything appearing in the cache, according to IGB.

Select bedgraph, bedgraph tabix, bigfwig, wig

On the initial loading of data, bedgraph tabix loads the fastest, followed by bigwig. bedgraph and wig take the longest. Unclear why bigwig takes longer than bedgraph tabix, as they are both indexed binary files. On subsequent loading of the files, all four files load in approximately the same amount of time, even with the cache disabled and the removal of the .igb folder.

Could this indicate that the initial retrieval of chromosomes for the files is what takes the most amount of time?

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Nowlan Freese added a comment - 14/Oct/21 2:26 PM - edited Testing in 9.1.8 release For files, use the above quickload hosted on CyVerse. In IGB Open the Arabidopsis thaliana genome A_thaliana_Jun_2009 Navigate to Chr1:2,257,247-2,260,234 Select bigBed, bed, bed tabix in the Available Data box I see no difference in loading times, with or without the cache enabled. I also don't see anything appearing in the cache, according to IGB. Select bedgraph, bedgraph tabix, bigfwig, wig On the initial loading of data, bedgraph tabix loads the fastest, followed by bigwig. bedgraph and wig take the longest. Unclear why bigwig takes longer than bedgraph tabix, as they are both indexed binary files. On subsequent loading of the files, all four files load in approximately the same amount of time, even with the cache disabled and the removal of the .igb folder. Could this indicate that the initial retrieval of chromosomes for the files is what takes the most amount of time?

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Nowlan Freese added a comment - 14/Oct/21 2:29 PM

Regarding the JASPAR2022_araTha1.bb file referenced in a previous comment, I am seeing the following exception when attempting to load the file.

java.lang.NullPointerException: null
at com.gene.bigbedhandler.BigBedSymLoader.getRegion(BigBedSymLoader.java:138) ~[na:na]
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.getRegion(QuickLoadSymLoader.java:287) ~[genometry-9.1.8.jar:na]
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:164) ~[genometry-9.1.8.jar:na]
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:139) ~[genometry-9.1.8.jar:na]
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:119) ~[genometry-9.1.8.jar:na]
at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:752) ~[igb-9.1.8.jar:na]
at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:694) [igb-9.1.8.jar:na]
at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:689) [igb-9.1.8.jar:na]
at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73) [genometry-9.1.8.jar:na]
at javax.swing.SwingWorker$1.call(SwingWorker.java:295) [na:1.8.0_241]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_241]
at javax.swing.SwingWorker.run(SwingWorker.java:334) [na:1.8.0_241]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [na:1.8.0_241]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [na:1.8.0_241]
at java.lang.Thread.run(Thread.java:748) [na:1.8.0_241]

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Nowlan Freese added a comment - 14/Oct/21 2:29 PM Regarding the JASPAR2022_araTha1.bb file referenced in a previous comment, I am seeing the following exception when attempting to load the file. java.lang.NullPointerException: null at com.gene.bigbedhandler.BigBedSymLoader.getRegion(BigBedSymLoader.java:138) ~ [na:na] at com.affymetrix.genometry.quickload.QuickLoadSymLoader.getRegion(QuickLoadSymLoader.java:287) ~ [genometry-9.1.8.jar:na] at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:164) ~ [genometry-9.1.8.jar:na] at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:139) ~ [genometry-9.1.8.jar:na] at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:119) ~ [genometry-9.1.8.jar:na] at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:752) ~ [igb-9.1.8.jar:na] at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:694) [igb-9.1.8.jar:na] at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:689) [igb-9.1.8.jar:na] at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73) [genometry-9.1.8.jar:na] at javax.swing.SwingWorker$1.call(SwingWorker.java:295) [na:1.8.0_241] at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_241] at javax.swing.SwingWorker.run(SwingWorker.java:334) [na:1.8.0_241] at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [na:1.8.0_241] at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [na:1.8.0_241] at java.lang.Thread.run(Thread.java:748) [na:1.8.0_241]

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Nowlan Freese added a comment - 14/Oct/21 3:31 PM

IGV 2.11.1 is able to load the data from http://expdata.cmmt.ubc.ca/JASPAR/downloads/UCSC_tracks/2022/JASPAR2022_araTha1.bb

I also downloaded the file and attempted to load in IGB - it failed with the same exception.

Using the UCSC bigBedToBed converter, I converted the JASPAR2022_araTha1.bb file to a bed file, gzipped, and tabix indexed it. This bed file was able to load correctly in IGB without issue. I also ran the UCSC bigBedInfo on the JASPAR2022_araTha1.bb file, and did not receive any errors.

This would indicate an issue with the IGB parsing of the file, though it is unclear why this bigBed fails to load while others load correctly.

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Nowlan Freese added a comment - 14/Oct/21 3:31 PM IGV 2.11.1 is able to load the data from http://expdata.cmmt.ubc.ca/JASPAR/downloads/UCSC_tracks/2022/JASPAR2022_araTha1.bb I also downloaded the file and attempted to load in IGB - it failed with the same exception. Using the UCSC bigBedToBed converter, I converted the JASPAR2022_araTha1.bb file to a bed file, gzipped, and tabix indexed it. This bed file was able to load correctly in IGB without issue. I also ran the UCSC bigBedInfo on the JASPAR2022_araTha1.bb file, and did not receive any errors. This would indicate an issue with the IGB parsing of the file, though it is unclear why this bigBed fails to load while others load correctly.

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Nowlan Freese added a comment - 14/Oct/21 3:51 PM

The JASPAR2022_araTha1.bb file has different chromosome names than the A_thaliana_Jun_2009 genome in IGB. My best guess is that the bigBed parser in IGB is failing to account for the different chromosome names.

chr1 0 30427671
chr2 1 19698289
chr3 2 23459830
chr4 3 18585056
chr5 4 26975502
chrCp 5 154478
chrMt 6 366924

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Nowlan Freese added a comment - 14/Oct/21 3:51 PM The JASPAR2022_araTha1.bb file has different chromosome names than the A_thaliana_Jun_2009 genome in IGB. My best guess is that the bigBed parser in IGB is failing to account for the different chromosome names. chr1 0 30427671 chr2 1 19698289 chr3 2 23459830 chr4 3 18585056 chr5 4 26975502 chrCp 5 154478 chrMt 6 366924

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Nowlan Freese added a comment - 14/Oct/21 4:08 PM

IGV does not show any data on the mitochondria chromosome (the sequence name should be ChrM, but the JASPAR2022_araTha1.bb file lists it as chrMt). IGB does show data for ChrM for the bed file version.

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Nowlan Freese added a comment - 14/Oct/21 4:08 PM IGV does not show any data on the mitochondria chromosome (the sequence name should be ChrM, but the JASPAR2022_araTha1.bb file lists it as chrMt). IGB does show data for ChrM for the bed file version.

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Nowlan Freese added a comment - 14/Oct/21 4:29 PM

I'm not seeing a significant difference in the time to load the same test files between IGB and IGV.

https://data.cyverse.org/dav-anon/iplant/home/nfreese/2954_testing/quickload/A_thaliana_Jun_2009/SRR10060893.bedgraph
https://data.cyverse.org/dav-anon/iplant/home/nfreese/2954_testing/quickload/A_thaliana_Jun_2009/SRR10060893.bedgraph.gz
https://data.cyverse.org/dav-anon/iplant/home/nfreese/2954_testing/quickload/A_thaliana_Jun_2009/SRR10060893.bedgraph.gz.tbi
https://data.cyverse.org/dav-anon/iplant/home/nfreese/2954_testing/quickload/A_thaliana_Jun_2009/SRR10060893.bigwig
https://data.cyverse.org/dav-anon/iplant/home/nfreese/2954_testing/quickload/A_thaliana_Jun_2009/SRR10060893.wig

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Nowlan Freese added a comment - 14/Oct/21 4:29 PM I'm not seeing a significant difference in the time to load the same test files between IGB and IGV. https://data.cyverse.org/dav-anon/iplant/home/nfreese/2954_testing/quickload/A_thaliana_Jun_2009/SRR10060893.bedgraph https://data.cyverse.org/dav-anon/iplant/home/nfreese/2954_testing/quickload/A_thaliana_Jun_2009/SRR10060893.bedgraph.gz https://data.cyverse.org/dav-anon/iplant/home/nfreese/2954_testing/quickload/A_thaliana_Jun_2009/SRR10060893.bedgraph.gz.tbi https://data.cyverse.org/dav-anon/iplant/home/nfreese/2954_testing/quickload/A_thaliana_Jun_2009/SRR10060893.bigwig https://data.cyverse.org/dav-anon/iplant/home/nfreese/2954_testing/quickload/A_thaliana_Jun_2009/SRR10060893.wig

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Ann Loraine added a comment - 15/Oct/21 10:05 AM

Question: Does IGB's on-board (included in the jar) chromosome synonym file contain the Jasper synonym(s)?

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Ann Loraine added a comment - 15/Oct/21 10:05 AM Question: Does IGB's on-board (included in the jar) chromosome synonym file contain the Jasper synonym(s)?

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Nowlan Freese added a comment - 15/Oct/21 4:28 PM - edited

Some of the JASPAR synonyms are part of the chromosomes.txt file. So, for example, when I load the bed file converted from the JASPAR file some of the data will load for some of the chromosomes (not chrCp as that is not in chromosomes.txt). Because none of the bigBed JASPAR data are able to load, this indicates to me that the bigBed logic in IGB is not using the chromosome synonyms logic.

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Nowlan Freese added a comment - 15/Oct/21 4:28 PM - edited Some of the JASPAR synonyms are part of the chromosomes.txt file. So, for example, when I load the bed file converted from the JASPAR file some of the data will load for some of the chromosomes (not chrCp as that is not in chromosomes.txt). Because none of the bigBed JASPAR data are able to load, this indicates to me that the bigBed logic in IGB is not using the chromosome synonyms logic.

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Nowlan Freese added a comment - 15/Oct/21 4:34 PM

I have created two new tickets (~~IGBF-2978~~ and IGBF-2979) to fix issues identified in this ticket.

Closing this ticket.

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Nowlan Freese added a comment - 15/Oct/21 4:34 PM I have created two new tickets ( IGBF-2978 and IGBF-2979 ) to fix issues identified in this ticket. Closing this ticket.

People

Assignee:

Nowlan Freese

Reporter:

Ann Loraine

Votes:

0 Vote for this issue

Watchers:

2 Start watching this issue

Dates

Created:

22/Sep/21 5:14 PM

Updated:

24/Mar/22 9:42 AM

Resolved:

15/Oct/21 4:34 PM