bam loading error_uneven line lengths in contig null

[Sepideh Alamouti]

Hello,
I have created a new genome using IGV, the latest version, and   IGV2.3.51command line. Loading a related sorted_indexed.bam file dump into an error in both IGV versions above. However I can load the same .bam file using IGV 2.1. Can you please help me to figure out what is the problem with my dataset not being loaded with the newer version of IGV?

Regards,
Sepideh M. Alamouti

Below, please find an example of the log error:

ERROR [2015-06-03 23:26:43,615]  [MessageUtils.java:50] [AWT-EventQueue-0]  An error occurred while accessing:    /Volumes/morinlab/projects/capp_seq_forme_fruste/help/refgenefusion_pog062_S17.PSort.rmdup.bam<br>Fasta file has uneven line lengths in contig null
org.broad.igv.exceptions.DataLoadException: An error occurred while accessing:    /Volumes/morinlab/projects/capp_seq_forme_fruste/help/refgenefusion_pog062_S17.PSort.rmdup.bam<br>Fasta file has uneven line lengths in contig null
    at org.broad.igv.feature.genome.FastaUtils.createIndexFile(FastaUtils.java:80)
    at org.broad.igv.feature.genome.GenomeManager.loadFastaFile(GenomeManager.java:275)
    at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:152)
    at org.broad.igv.ui.IGV.loadGenome(IGV.java:671)
    at org.broad.igv.ui.IGV.loadGenome(IGV.java:652)
    at org.broad.igv.ui.IGV.doLoadGenome(IGV.java:620)
    at org.broad.igv.ui.IGVMenuBar$11.actionPerformed(IGVMenuBar.java:534)
    at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
    at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
    at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
    at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
    at javax.swing.AbstractButton.doClick(AbstractButton.java:389)
    at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:809)
    at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:137)
    at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:850)
    at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272)
    at java.awt.Component.processMouseEvent(Component.java:6414)
    at javax.swing.JComponent.processMouseEvent(JComponent.java:3275)
    at java.awt.Component.processEvent(Component.java:6179)
    at java.awt.Container.processEvent(Container.java:2084)
    at java.awt.Component.dispatchEventImpl(Component.java:4776)
    at java.awt.Container.dispatchEventImpl(Container.java:2142)
    at java.awt.Component.dispatchEvent(Component.java:4604)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4618)
    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4279)
    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4209)
    at java.awt.Container.dispatchEventImpl(Container.java:2128)
    at java.awt.Window.dispatchEventImpl(Window.java:2492)
    at java.awt.Component.dispatchEvent(Component.java:4604)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:717)
    at java.awt.EventQueue.access$400(EventQueue.java:82)
    at java.awt.EventQueue$2.run(EventQueue.java:676)
    at java.awt.EventQueue$2.run(EventQueue.java:674)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
    at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:97)
    at java.awt.EventQueue$3.run(EventQueue.java:690)
    at java.awt.EventQueue$3.run(EventQueue.java:688)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:687)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
ERROR [2015-06-03 23:26:43,617]  [MessageUtils.java:60] [AWT-EventQueue-0]  An error occurred while accessing:  bam<br>Fasta file has uneven line lengths in contig null

[Jim Robinson]

Hi,

The problem is with your fasta file, not the BAM file.  Each  line in the fasta file has to be the same length,  with the exception of the last line of each sequence. 

Jim

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/30d502e8-ef67-4047-8a40-1334ffc87824%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[sepideh]

Hi Jim,

Thank you for the response. Adjusting the fasta width length, resolved the issue.

Regards,

Sepideh

You received this message because you are subscribed to a topic in the Google Groups "igv-help" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/igv-help/dFqoGOYrR-o/unsubscribe.
To unsubscribe from this group and all its topics, send an email to igv-help+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/55704DAB.9060900%40broadinstitute.org.

[Jim Robinson]

Thanks for letting us know.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/E48ACF89-6929-4E38-BEB9-12BE52BF91DF%40gmail.com.

[sepideh alamouti]

Hello,

After your response, I checked the files using IGV 2.1 (by mistake) that’s why I thought the problem is related to my fasta line. But it seems that’s a null error log. I got rid of all the break line in my fasta and still get the same error.

Would you please look at the example file? 

Regards,

Sepideh

 

[Jim Robinson]

Hi,

This fasta is fine.    I don't understand the reference to IGV 2.1,  but are you still having problems with the latest release?

Jim

--

[sepideh alamouti]

Hi Jim,

I’m still having problem with the latest release to load the alignment file using this fasta as a new genome. 

Thank you,

Sepideh

--

---
You received this message because you are subscribed to a topic in the Google Groups "igv-help" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/igv-help/dFqoGOYrR-o/unsubscribe.
To unsubscribe from this group and all its topics, send an email to igv-help+u...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/557115F8.5000904%40broadinstitute.org.

[Jim Robinson]

Hi Sepideh,  please delete you igv.log file, then start igv again, try your load, and send me the resulting log file.   Also, exact steps you are taking in sequence, such as "select Genome > Load genome from file...",  etc,   I can't really guess what you are doing so the more precise the better chance I have to help you.

Jim

You received this message because you are subscribed to the Google Groups "igv-help" group.

To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/24B410CE-F89E-423A-BA46-D6E621CE4E15%40gmail.com.

[sepideh alamouti]

Dear Jim,

The steps I’m taking are as follow:

Create .genome file > FASTA file (Browse) > File > Load from file > .bam . I have tried the same process with the same files using IGV2.1 and had no problem.

Below, please find the .log file form IGV2.3.52. 

[Jim Robinson]

This is really curious, the only error I see would be triggered by an annotation file,  specifically a refGene or other UCSC format

java.lang.ArrayIndexOutOfBoundsException: 4
    at org.broad.igv.feature.tribble.UCSCGeneTableCodec.decode(UCSCGeneTableCodec.java:113)
    at org.broad.igv.feature.tribble.UCSCGeneTableCodec.decode(UCSCGeneTableCodec.java:27)

Are you multi-selecting the bam and another file?  

Is it possible to extract a small portion of this bam that will reproduce the problem and share it with me?  I can give you a private ftp to upload to, or download it from your server.   Without something to reproduce the problem there's not much more I can do.

I will be out the rest of the day, and in general for the next several days,  but will respond when I can.

Jim

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/1371F6DE-428F-4EF0-A6D9-397B607BBBAB%40gmail.com.

For more options, visit https://groups.google.com/d/optout.

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/1371F6DE-428F-4EF0-A6D9-397B607BBBAB%40gmail.com.

For more options, visit https://groups.google.com/d/optout.

Regards,

Sepideh

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/5571BB72.2010603%40broadinstitute.org.

For more options, visit https://groups.google.com/d/optout.

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/1371F6DE-428F-4EF0-A6D9-397B607BBBAB%40gmail.com.

[sepideh alamouti]

Thank you Jim, if you send me the ftp address I can upload the bam file. 

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/5571DF1C.9070205%40broadinstitute.org.

[Jim Robinson]

Hi,

FTP instructions are below.  Please let us know when they are there so we can retrieve them.  If you are using a ".genome" file  please upload that also. 

My colleague pointed out that you might have selected the bam file as the "annotation" file when creating the .genome file.   If you did that would explain the symptoms,  Is that possible?

Jim

Our external public ftp site address is ftp.broadinstitute.org. A user logs in with a username of anonymous and a password of their email address.

Once connected, the user can upload the data to the incoming directory  (NOTE:  you must "cd incoming"). This upload directory is a blind directory, i.e. after the upload is done, the file that was uploaded, or any file in the incoming directory, cannot be read.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/D658FF04-C997-4E01-9912-5BE903693B6A%40gmail.com.

[sepideh alamouti]

Hi Jim,

I have a “.genome" and a related “alignment.bam” files uploaded into /incoming/sepidehalamouti/. 

PS) I have not selected the bam file as the ‘annotation’ file. I can load the same files using IGV2.1 but not the latest version so I believe the steps I’m taking are alright.

Many thanks,

Sepideh

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/55726189.2020807%40broadinstitute.org.

[Jim Robinson]

Hi Sepideh,

Unfotunately it loads just fine for me (see screenshot).   The only other thing I can suggest is that you quit igv,  delete (or mv) your "igv" folder, then restart and try again.   BTW,  you do not need to create a ".genome" file,  just load the fasta using  "Load Genome from File". 

Jim

[sepideh]

Hi Jim,

Thank you for looking into the loading error issue. I did some trials and errors to figure out the problem from my end. Since I had not sent you the index .bam, first I suspected the version of my samtools (0.1.19). But finally I noticed that the problem is caused by IGV not liking a long 'filename. As soon as I shorten my filenames, everything start working nicely!!

Regards,

Sepideh M. Alamouti

  

On 2015-06-05, at 10:28 PM, Jim Robinson wrote:

Hi Sepideh,

Unfotunately it loads just fine for me (see screenshot).   The only other thing I can suggest is that you quit igv,  delete (or mv) your "igv" folder, then restart and try again.   BTW,  you do not need to create a ".genome" file,  just load the fasta using  "Load Genome from File". 

Jim

<Screen Shot 2015-06-05 at 10.24.50 PM.png>

Hi Jim,

I have a “.genome" and a related “alignment.bam” files uploaded into /incoming/sepidehalamouti/. 

PS) I have not selected the bam file as the ‘annotation’ file. I can load the same files using IGV2.1 but not the latest version so I believe the steps I’m taking are alright.

Many thanks,

Sepideh

--

---
You received this message because you are subscribed to a topic in the Google Groups "igv-help" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/igv-help/dFqoGOYrR-o/unsubscribe.
To unsubscribe from this group and all its topics, send an email to igv-help+u...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/55728500.7060709%40broadinstitute.org.