Entering edit mode
11.7 years ago
stu.andrews
•
0
For some unexplained reason, the bedGraphToBigWig utility fails to successfully convert some of the inputs I provide. For example, I am running
bedGraphToBigWig test.bedGraph chrom_sizes.txt test.bw
with the following input file (test.bedGraph),
1 99213343 99213420 1
1 99213555 99213579 1
1 101812951 101813052 1
1 104285951 104285953 1
1 104285953 104285954 3
1 104285954 104285956 4
1 104285956 104285978 5
1 104285978 104285979 3
and a chromosome sizes file (chrom_sizes.txt),
1 135534747
the tool runs without error generating a BigWig file that is well-formed but appears empty, according to bigWigInfo:
bigWigInfo test.bw
version: 4
isCompressed: yes
isSwapped: 0
primaryDataSize: 90
zoomLevels: 0
chromCount: 1
basesCovered: 0
mean: nan
min: 0.000000
max: 0.000000
std: nan
and will not load into IGV. To add to the mystery, I can duplicate the original file with bigWigToBedGraph test.bw test1.bedGraph.
This is on a Mac computer running ML with up to date software.
Does anyone have a clue as to what's going on?
Your help would be much appreciated.
S.
Try replacing 1 with chr1, IGV might not be able to pick it up + how are you loading the bigwig in IGV, I used to do it with an Url
Hi Sukhdeep, This doesn't look like a naming issue for a couple of reasons. First, I have successfully loaded other sections of the same input file using the same conversion to bigwig, and the same "Load from file ..." dialog. And second, IGV throws an exception while retrieving zoom-level data (see below) which is one of the auspicious-looking fields in bigWigInfo shown above.
If possible, could you confirm that the conversion to bigwig works/doesn't work on your system? Keep in mind that the input columns are tab-separated.
Thanks for your response. - S.
ERROR [2013-02-27 18:10:49,973] [IGV.java:1491] [pool-1-thread-5] Error loading tracks java.lang.NullPointerException at org.broad.igv.bigwig.BigWigDataSource.getZoomLevelForScale(BigWigDataSource.java:179) at org.broad.igv.bigwig.BigWigDataSource.initMinMax(BigWigDataSource.java:96) at org.broad.igv.bigwig.BigWigDataSource.<init>(BigWigDataSource.java:70) at org.broad.igv.track.TrackLoader.loadBWFile(TrackLoader.java:758) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:213) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:101) at org.broad.igv.ui.IGV.load(IGV.java:1529) at org.broad.igv.ui.IGV$10.run(IGV.java:1473) at org.broad.igv.ui.IGV.loadResources(IGV.java:1500) at org.broad.igv.ui.IGV$4.run(IGV.java:618) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:54) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918) at java.lang.Thread.run(Thread.java:680) INFO [2013-02-27 18:10:49,974] [MessageUtils.java:60] [pool-1-thread-5] Error loading /Users/stu/Research/Pathology/Axin/TanHang/UNMAPPED/tohuman/HS85/SamplesPlusfiltered_thout-1/test.bw: null
Strange, I would suggest you asking the IGV google group, post, there might be an encoding issue or some problem with input bedGraph file.