NullPointerException problem

[L1feone]

Hi!

I mapped paired end library to a genome. Now I am trying to visualise it via IGV, but I am always getting this message when trying to jump to a certain chromosome: "Error encountered querying alignments: java.lang.NullPointerException". Reference genome has 19 chromosomes and a lot of unplaced genomic scaffolds. Jumping to these scaffolds does not cause an error. Only when I am picking a chromosome. Bam file is sorted and indexed, Reference file headers and bam headers are same and in the same order.

Tablet and IGB don't have these problems, but I want to use IGV.

I found a few old topics in the internet with the same problem, but didn't find any solution.

Help please.

Thank you.

[jrobinso]

Hi, you posted in igv.js, is this about the javascript component or the desktop application?

[L1feone]

Hi, it is about desktop application

[jrobinso]

This is not the correct repository, I will move it.

I will need to know the version of IGV you are using, and also the contents of the "igv.log" file, it is in the "igv" folder in your home directory. If you are able to share the BAM file that would be helpful.

[L1feone]

IGV version is 2.8.2
BAM file is 32mb so I uploaded it do google disc:

https://drive.google.com/file/d/1ff2mEB1oPrnSGelQEvSbWCcw9KsPBisc/view?usp=sharing

[jrobinso]

What locus (genome location) do you encounter this error? Is the bam file indexed?

[L1feone]

BAM file indexed. Error occures with every chromosome wich name starts with NC_######

[jrobinso]

I need a fasta file to load this. Is the fasta reference available online?

[L1feone]

Yes, here it is:

https://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_other/Nothobranchius_furzeri/latest_assembly_versions/GCF_001465895.1_Nfu_20140520/GCF_001465895.1_Nfu_20140520_genomic.fna.gz

[jrobinso]

OK I downloaded the fasta for one of the sequences, NC_029651.1, and was able to load the file with no problem. I went to locus NC_029651.1:12,142,889-12,146,819 (see screenshot). To look into this further I need exact steps from you to reproduce, including a locus that reproduces the problem. Also, as I requested earlier, the contents of igv.log would be helpful. Its in an "igv" folder in your home directory. When you've supplied these things I will look further. Thanks for your report.

[L1feone]

igv.log

[L1feone]

I just tried IGV 2.8.0 and everything worked out well.

[jrobinso]

@L1feone could you answer my question re an exact locus to reproduce the problem?

[jrobinso]

And another question, what is you "visibility window" for alignments set to?

[jrobinso]

OK I think I see the issue from your igv.log file. This bug will occur in bam files without base qualities if a large visibility window is set. A fix was pushed for it on April 7 but it is not released. If 2.8.0 is working you can continue using that, or you can use the snapshot build from here: https://software.broadinstitute.org/software/igv/download_snapshot until the next release, sometime in June.

[L1feone]

Ok, thank you!
I will try the snapshot build.

By the way, an error occured with standart visibility window too. Should i still describe the specific steps which led to an error?

[jrobinso]

@L1feone Yes if you don't mind, and I will test your steps to reproduce. Its possible there is a separate bug.

Warning about the snapshot build, it is by its nature not stable, if you don't need features added since 2.8.0 I would stick with that version.

[L1feone]

Ok, 2.8.0 suits me well)

My steps are:
After opening IGV and choosing the genome I am loading my BAM file. Error occures when I choos a NC_###### chromosome. Choosing NW_####### doesn't couse any errors and I can see my aligned sequences. Error occures both on linux and windows.

[jrobinso]

This should be fixed with release 2.8.3