Error trying to load bigwig files
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Todd Creasy
Jan 18, 2012, 11:04:48 AM1/18/12
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I'm trying to load a bigwig file from a server and I keep getting error that it can't load. Below is the error log. Looks like there is a problem with a header. I created the bigwig's from bedgraph files that DO have a header in them (below). Am I missing something?
track type=bedGraph name=track_label description=center_label color=255,0,0
ERROR [2012-01-18 10:57:04,620] [HTTPHelper.java:72] Error (Not Found ) fetching content length: [REMOVED_URL]/R26F_G19F_Cre_1.accepted_hits.sorted_by_position.coverage.bw
ERROR [2012-01-18 10:57:04,670] [TrackLoader.java:269] java.lang.RuntimeException: Error reading file header for [REMOVED_URL]/R26F_G19F_Cre_1.accepted_hits.sorted_by_position.coverage.bw
ERROR [2012-01-18 10:57:04,672] [IGV.java:1462] Error loading tracks
org.broad.igv.exceptions.DataLoadException: <html>An error occurred while accessing: [REMOVED_URL]/R26F_G19F_Cre_1.accepted_hits.sorted_by_position.coverage.bw<br>Error reading file header for [REMOVED_URL]/R26F_G19F_Cre_1.accepted_hits.sorted_by_position.coverage.bw
at org.broad.igv.track.TrackLoader.load(TrackLoader.java:270)
at org.broad.igv.ui.IGV.load(IGV.java:1501)
at org.broad.igv.ui.IGV$10.run(IGV.java:1444)
at org.broad.igv.ui.IGV.loadResources(IGV.java:1471)
at org.broad.igv.ui.IGV$4.run(IGV.java:630)
at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:74)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:680)
track type=bedGraph name=track_label description=center_label color=255,0,0
ERROR [2012-01-18 10:57:04,620] [HTTPHelper.java:72] Error (Not Found ) fetching content length: [REMOVED_URL]/R26F_G19F_Cre_1.accepted_hits.sorted_by_position.coverage.bw
ERROR [2012-01-18 10:57:04,670] [TrackLoader.java:269] java.lang.RuntimeException: Error reading file header for [REMOVED_URL]/R26F_G19F_Cre_1.accepted_hits.sorted_by_position.coverage.bw
ERROR [2012-01-18 10:57:04,672] [IGV.java:1462] Error loading tracks
org.broad.igv.exceptions.DataLoadException: <html>An error occurred while accessing: [REMOVED_URL]/R26F_G19F_Cre_1.accepted_hits.sorted_by_position.coverage.bw<br>Error reading file header for [REMOVED_URL]/R26F_G19F_Cre_1.accepted_hits.sorted_by_position.coverage.bw
at org.broad.igv.track.TrackLoader.load(TrackLoader.java:270)
at org.broad.igv.ui.IGV.load(IGV.java:1501)
at org.broad.igv.ui.IGV$10.run(IGV.java:1444)
at org.broad.igv.ui.IGV.loadResources(IGV.java:1471)
at org.broad.igv.ui.IGV$4.run(IGV.java:630)
at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:74)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:680)
Jim Robinson
Jan 18, 2012, 11:09:42 AM1/18/12
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Hi Todd,
How did you create the bigwig file? I was not aware you could use
bedgraph format for bigwig, did you first convert it to wig (see
http://genome.ucsc.edu/goldenPath/help/bigWig.html). Secondly, the
same site explicitly says you must remove track lines beforehand. So
perhaps the bigwig is corrupt?
Jim
Todd Creasy
Jan 18, 2012, 11:13:41 AM1/18/12
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Hi Jim,
You're right about the track line. However, I tried with and without the track line with the same problem. You can use bedGraphToBigWig to create bw's from bg's. This is from the url you sent me:
Wiggle data must be continuous and the elements must be equally sized. If your data is sparse or contains elements of varying size, use the bedGraph format instead of the wiggle format. If you have a very large bedGraph data set, you can convert it to the bigWig format using the bedGraphToBigWig program. For details, see Example Three below.
You're right about the track line. However, I tried with and without the track line with the same problem. You can use bedGraphToBigWig to create bw's from bg's. This is from the url you sent me:
Wiggle data must be continuous and the elements must be equally sized. If your data is sparse or contains elements of varying size, use the bedGraph format instead of the wiggle format. If you have a very large bedGraph data set, you can convert it to the bigWig format using the bedGraphToBigWig program. For details, see Example Three below.
Todd Creasy
Jan 18, 2012, 11:45:17 AM1/18/12
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It is possible the problem lies within the creation of the bedgraph file from a bam. I used this command from bedtools:
genomeCoverageBed -bg -split -ibam $file -g $chrom_sizes
genomeCoverageBed -bg -split -ibam $file -g $chrom_sizes
James Robinson
Jan 18, 2012, 11:58:18 AM1/18/12
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Todd,
I will probably need to see the file to debug further. We're are having trouble with our dropbox, if I send ftp instructions could you send them to us?
Have you tried loading this track at UCSC? I have found the the wigToBigwig program fails at times with no warning, leaving a corrupt file.
Jim
I will probably need to see the file to debug further. We're are having trouble with our dropbox, if I send ftp instructions could you send them to us?
Have you tried loading this track at UCSC? I have found the the wigToBigwig program fails at times with no warning, leaving a corrupt file.
Jim
On Wed, Jan 18, 2012 at 11:54 AM, Jim Robinson <jrob...@broadinstitute.org> wrote:
Todd,
I will probably need to see the file to debug further. We're are having trouble with our dropbox, if I send ftp instructions could you send them to us?
Have you tried loading this track at UCSC? I have found the the wigToBigwig program fails at times with no warning, leaving a corrupt file.
Jim
Todd Creasy
Jan 18, 2012, 12:00:25 PM1/18/12
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Sure, send me the ftp site. But just as a reminder, I didn't use wigToBigwig. I used bedGraphToBigWig. I'll ftp over a README of what I did.
Jim Robinson
Jan 18, 2012, 11:55:00 AM1/18/12
to igv-...@googlegroups.com
Todd,
I will probably need to see the file to debug further. We're are having trouble with our dropbox, if I send ftp instructions could you send them to us?
Have you tried loading this track at UCSC? I have found the the wigToBigwig program fails at times with no warning, leaving a corrupt file.
Jim
I will probably need to see the file to debug further. We're are having trouble with our dropbox, if I send ftp instructions could you send them to us?
Have you tried loading this track at UCSC? I have found the the wigToBigwig program fails at times with no warning, leaving a corrupt file.
Jim
Giovanni Marsico
Mar 20, 2014, 7:24:42 AM3/20/14
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Dear Jim and Todd,
I am currently having the same problem: I created a bigwig from a bedgraph file using the ucsc command "bedGraphToBigWig".
When I try to laod it in IGV 2.3 I get this error:
"Error loading ...: Error reading
BBFile header for: ..."Any help with this would be much appreciated.
Thanks,
Giovanni Marsico
Jim Robinson
Mar 20, 2014, 8:29:29 AM3/20/14
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Please verify that you are using the
latest version of IGV (2.3.32). You can check the version by
selecting "Help > About" from the menu.
Jim
Jim
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Boxiang Liu
Jul 8, 2016, 10:23:20 PM7/8/16
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Hello Jim, I am having the same problem. I am using version 2.3.78.
Jim Robinson
Jul 8, 2016, 10:31:21 PM7/8/16
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OK, I'll need a file that can reproduce this problem along with
steps to reproduce to make any progress. Also your igv.log file.
In general referencing old emails and saying "I am having the same
problem" is not very helpful, most of the time it turns out to not
be the same problem.
Can you reproduce the problem with a reasonable size file you can share? I can send you a dropbox link for upload if you can.
Can you reproduce the problem with a reasonable size file you can share? I can send you a dropbox link for upload if you can.
janeenbr...@gmail.com
Jul 5, 2020, 8:54:37 PM7/5/20
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Hello I am having this issues right now. How to solve the problem.
Message has been deleted
Emily E.T.
Oct 17, 2023, 12:16:32 AM10/17/23
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I had this problem but after removing rows with MtDNA and adding back the "chr" prefix before converting the bedgraph to bigwig it can be opened by IGV finally, thx God
igv-help
Oct 19, 2023, 9:14:05 PM10/19/23
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Well, as I explained above the first step is to upload a file to reproduce the problem.
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