create .genome does not work,why?

[luxi...@126.com]

I use the igv of version 2.3.90 in windows system to create the zea mays genome v4 and download the fa and gff3 files from Ensembl_Genomes.but after the genome file was created , the igv cannot load it and the computer was almost crashed.my computer is very new and expensive.but if I download the OSgenome fa and gff3 file,the igv works well.if I get rid of some chromosomes of the files, the igv works well,as if the igv cannot deal with large data. The problem remains in the ubuntu. can anybody help me? The log is as follows:

ERROR [2017-01-25 17:26:58,077] [IGVCommandBar.java:285]  Error initializing genome
java.lang.NullPointerException
 at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:156)
 at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:129)
 at org.broad.igv.ui.IGVCommandBar$4.run(IGVCommandBar.java:250)
 at org.broad.igv.util.LongRunningTask.submit(LongRunningTask.java:57)
 at org.broad.igv.ui.IGVCommandBar.loadGenomeListItem(IGVCommandBar.java:297)
 at org.broad.igv.ui.IGVCommandBar.access$500(IGVCommandBar.java:83)
 at org.broad.igv.ui.IGVCommandBar$GenomeBoxActionListener.actionPerformed(IGVCommandBar.java:308)
 at javax.swing.JComboBox.fireActionEvent(JComboBox.java:1258)
 at javax.swing.JComboBox.setSelectedItem(JComboBox.java:586)
 at org.broad.igv.ui.IGVCommandBar.selectGenome(IGVCommandBar.java:541)
 at org.broad.igv.ui.IGV$StartupRunnable.run(IGV.java:2519)
 at org.broad.igv.util.LongRunningTask.submit(LongRunningTask.java:57)
 at org.broad.igv.ui.IGV.startUp(IGV.java:2462)
 at org.broad.igv.ui.Main.open(Main.java:274)
 at org.broad.igv.ui.Main.main(Main.java:94)
INFO [2017-01-25 17:26:58,219] [CommandListener.java:106]  Listening on port 60151
INFO [2017-01-25 18:04:53,307] [ShutdownThread.java:51]  Shutting down

[James Robinson]

Could you attach the .genome file that is causing the error in the log above?  It looks like a problem occurred in creation of the file.

For large gff files do not create a ".genome" file.   Rather load the fasta file directly to define the reference genome using "Genome > Load from file".    Then load the gff separately from the File menu, but first sort and index it using either igvtools or tabix.   The reason for this is that  the entire gff file must be loaded into memory from a .genome file.  In contrast an indexed gff can be loaded in pieces as needed.

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[James Robinson]

Hi,  I assume you me ".gff" file.  It will sort and index,  it might take a little time.  The warning message is normal.

On Wed, Jan 25, 2017 at 8:11 AM, <luxi...@126.com> wrote:

在 2017年1月25日星期三 UTC+8下午11:40:37，Jim Robinson写道：

Could you attach the .genome file that is causing the error in the log above?  It looks like a problem occurred in creation of the file.

For large gff files do not create a ".genome" file.   Rather load the fasta file directly to define the reference genome using "Genome > Load from file".    Then load the gff separately from the File menu, but first sort and index it using either igvtools or tabix.   The reason for this is that  the entire gff file must be loaded into memory from a .genome file.  In contrast an indexed gff can be loaded in pieces as needed.

On Wed, Jan 25, 2017 at 2:22 AM, <luxi...@126.com> wrote:

I use the igv of version 2.3.90 in windows system to create the zea mays genome v4 and download the fa and gff3 files from Ensembl_Genomes.but after the genome file was created , the igv cannot load it and the computer was almost crashed.my computer is very new and expensive.but if I download the OSgenome fa and gff3 file,the igv works well.if I get rid of some chromosomes of the files, the igv works well,as if the igv cannot deal with large data. The problem remains in the ubuntu. can anybody help me? The log is as follows:

ERROR [2017-01-25 17:26:58,077] [IGVCommandBar.java:285]  Error initializing genome
java.lang.NullPointerException
 at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:156)
 at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:129)
 at org.broad.igv.ui.IGVCommandBar$4.run(IGVCommandBar.java:250)
 at org.broad.igv.util.LongRunningTask.submit(LongRunningTask.java:57)
 at org.broad.igv.ui.IGVCommandBar.loadGenomeListItem(IGVCommandBar.java:297)
 at org.broad.igv.ui.IGVCommandBar.access$500(IGVCommandBar.java:83)
 at org.broad.igv.ui.IGVCommandBar$GenomeBoxActionListener.actionPerformed(IGVCommandBar.java:308)
 at javax.swing.JComboBox.fireActionEvent(JComboBox.java:1258)
 at javax.swing.JComboBox.setSelectedItem(JComboBox.java:586)
 at org.broad.igv.ui.IGVCommandBar.selectGenome(IGVCommandBar.java:541)
 at org.broad.igv.ui.IGV$StartupRunnable.run(IGV.java:2519)
 at org.broad.igv.util.LongRunningTask.submit(LongRunningTask.java:57)
 at org.broad.igv.ui.IGV.startUp(IGV.java:2462)
 at org.broad.igv.ui.Main.open(Main.java:274)
 at org.broad.igv.ui.Main.main(Main.java:94)
INFO [2017-01-25 17:26:58,219] [CommandListener.java:106]  Listening on port 60151
INFO [2017-01-25 18:04:53,307] [ShutdownThread.java:51]  Shutting down

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--- The .tff file is downloaded from website and is too large to be uploaded. I tried to sort and index it, but The warning messege of "Snappy is disabled via system property" showed up. I regard it as the compatibility between the .tff file and the igv. So I decided to try my best to program my own software to deal it. 

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[luxi...@126.com]

Can you give some example file of .gff3 and fa for creating the .genome, so we can find the reason about the problem? The difficulty for us to use the igv is that no example files exist.

    Li Yuan 

From ShenYang Agriculture University, China. Thanks a lot.

[James Robinson]

There are many example gff files,  just do a web search.   Again if you read my advice do not create a .genome file,   it is not needed,  just use the fasta for a reference.

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[luxi...@126.com]

Hi, I finally sorted and indexed the .gff file. But when I Load the sorted file, an error occured, the warning message of "Error loading *.sorted .gff3: java.lang.reflect.InvocationTargetException" showed up. I really installed the right version of java 64_bit and windows 64_bit, how this happened? The .gff file was downloaded from Ensembl_Genomes about the zea mays. I want to a .genome file of v4, but the .genome file from the server is v3.

在 2017年1月26日星期四 UTC+8下午12:28:22，Jim Robinson写道：

There are many example gff files,  just do a web search.   Again if you read my advice do not create a .genome file,   it is not needed,  just use the fasta for a reference.

On Wed, Jan 25, 2017 at 8:08 PM, <luxi...@126.com> wrote:

Can you give some example file of .gff3 and fa for creating the .genome, so we can find the reason about the problem? The difficulty for us to use the igv is that no example files exist.

    Li Yuan 

From ShenYang Agriculture University, China. Thanks a lot.

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[James Robinson]

Please attach your igv.log file.   Also, please give me a web link to the fasta and gff3 file you are trying to load. 

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[luxi...@126.com]

ftp://ftp.ensemblgenomes.org/pub/release-34/plants/fasta/zea_mays/dna/Zea_mays.AGPv4.dna.toplevel.fa.gz

ftp://ftp.ensemblgenomes.org/pub/release-34/plants/gff3/zea_mays/Zea_mays.AGPv4.34.gff3.gz

在 2017年1月26日星期四 UTC+8下午1:09:30，Jim Robinson写道：

Please attach your igv.log file.   Also, please give me a web link to the fasta and gff3 file you are trying to load. 

On Wed, Jan 25, 2017 at 8:54 PM, <luxi...@126.com> wrote:

Hi, I finally sorted and indexed the .gff file. But when I Load the sorted file, an error occured, the warning message of "Error loading *.sorted .gff3: java.lang.reflect.InvocationTargetException" showed up. I really installed the right version of java 64_bit and windows 64_bit, how this happened? The .gff file was downloaded from Ensembl_Genomes about the zea mays. I want to a .genome file of v4, but the .genome file from the server is v3.

在 2017年1月26日星期四 UTC+8下午12:28:22，Jim Robinson写道：

There are many example gff files,  just do a web search.   Again if you read my advice do not create a .genome file,   it is not needed,  just use the fasta for a reference.

On Wed, Jan 25, 2017 at 8:08 PM, <luxi...@126.com> wrote:

Can you give some example file of .gff3 and fa for creating the .genome, so we can find the reason about the problem? The difficulty for us to use the igv is that no example files exist.

    Li Yuan 

From ShenYang Agriculture University, China. Thanks a lot.

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[James Robinson]

Sorry I can't reproduce your problem.  I downloaded the files,  sorted and indexed the gff, and this is what I see (below).   From your log it looks like your igv build is corrupt.   How exactly did you install IGV?  Give exact steps,  including which button or option you clicked on the downloads page.

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[luxi...@126.com]

http://data.broadinstitute.org/igv/projects/downloads/IGV_2.3.90.exe， this is what I have downloaded.

then, I run the exe, unzip the file to the desktop, the click the igv.bat, start the igv.

then, Load genome from the file, load the .fa

then, run igvtool, sort and index the gff3

then, file, load from  file, load the gff3.

now, I really confused about this problem.

thanks.

在 2017年1月26日星期四 UTC+8下午1:46:16，Jim Robinson写道：

[luxi...@126.com]

I probably found the reason for this problem that there are chinese characters in the path name of the folder, for example, "C:\Users\Luxiya444\桌面文件夹\Zea_mays.AGPv4.34.sorted.gff3". I changed the chinese characters to the english, the warning message did not show up again. I thanks Jim for the kindness to help me sovle the problem.

Li Yuan and my colleague,  with our best regard

ShenYang Agriculture University, China.

[James Robinson]

Hi, try this.  Select "File > Load from URL" and paste this in

https://s3.amazonaws.com/igv.broadinstitute.org/data/Zea_mays.AGPv4.34/Zea_mays.AGPv4.34.sorted.gff3

[James Robinson]

Or download this locally and try using it

https://s3.amazonaws.com/igv.broadinstitute.org/data/Zea_mays.AGPv4.34/Zea_mays.AGPv4.34.sorted.gff3

https://s3.amazonaws.com/igv.broadinstitute.org/data/Zea_mays.AGPv4.34/Zea_mays.AGPv4.34.sorted.gff3.idx

[luxi...@126.com]

your .gff file showed no warning, but the size of your .gff file is not same as mine. I found that,  if the .gff file is in the folder with chinese characters name, then run igvtool to sort and index it, the sorted file will show warning message. if the folder with english name, no warning will show up. I compared Both .sorted files with Beyond Compare, no difference was found, but the idx files were found different in the first line, so I think the solve method is that do not use chinese folder name when run igvtool. It is same in the Ubuntu 16 of english version.

the files about this problem is below:

http://pan.baidu.com/s/1slS16c1

在 2017年1月27日星期五 UTC+8上午12:28:27，Jim Robinson写道：

[James Robinson]

OK, thanks for the information.   Chinese characters are not allowed in many or most genomic file formats, of course, but I did not realize there was a restriction on folder and file names.

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