Error loading features for interval: "chr location" ...java.lang.NullPointerException

[Ivan DOrso]

Everything was working perfectly with my IGV 2.0 run on a Mac OS X 10.6.8 (Snow Leopard)

Suddenly, while opening a sessions that previously was running great, this message poped-up:

Error loading features for interval: "any chr location" ...java.lang.NullPointerException

Whenever I move to a new location, the same message appears with the updated chr location

I don't know what to do since I haven't changed any set up. Same IGV 2.0 version and same Java.

Any input would be much appreciated!

Thanks,

Ivan-

[Jim Robinson]

Hi,

Could you verify the version you are running by selecting "help > about" from the menu?

Jim

[Kenneth Daily]

I'm having this error as well when I index with bgzip/tabix or with igvtools. I'm using 2.3.3, but got the exact same error with 2.1.18.

[Jim Robinson]

Hi,

I need more info.  At a minimum your igv.log file or stacktrace.  Also, it would be helpful if you could try the latest IGV (2.3.23) and reproduce the problem there, then send the log. 

Thanks

Jim

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[Kenneth Daily]

Thanks for the quick response! I'm actually getting a different error now, not sure what changed. You can see stack trace here:

https://gist.github.com/kdaily/4d64d56fc95e17c9eafb

Sorry, I meant 2.3.23 (just downloaded today). Using igvtools 2.3.20.

Strangely, this happens on post-processed files. I have VCF files output from MuTect and I've tried using snpEff filter and GATK SelectVariants to get a subset and then index; neither of these load. Something like:

# This doesn't load in IGV

cat test.vcf | java -jar SnpSift.jar filter "(FILTER = 'PASS')" > keep/test.vcf 

igvtools index keep/test.vcf

 

If I just use grep to get the correct variants out and then index, it loads just fine!

# This loads in IGV

grep "^#" test.vcf > keep/test.vcf

grep "chr.*PASS" test.vcf >> keep/test.vcf

igvtools index keep/test.vcf

[Kenneth Daily]

I think I left out some important information in the process of anonymizing my output - my original file name is '02.vcf' and this does not load in IGV. If I change the name to 02test.vcf, I can process it any way I want and it indexes and loads just fine. Maybe there is a regex not working properly that gets the filename to load the index?

Thanks.

[Jacob Silterra]

Hi Kenneth,

Are you seeing errors when you try to create the index for the VCF file, or when you try to load the VCF in IGV? From the stacktrace it looks like the index file is malformed, which could happen as a result of a malformed input VCF file. Can you send the file you're trying to index (so that would be AFTER filtering)? You can upload it to ftp.broadinstitute.org/incoming, a read-only ftp site. Feel free to include the file before filtering too, but note that we don't support SnpEff or GATK on this particular mailing list.

Another thing to try would be doing a diff between the files that apparently function and those which don't:

# This doesn't load in IGV

cat test.vcf | java -jar SnpSift.jar filter "(FILTER = 'PASS')" > keep/test_a.vcf 

igvtools index keep/test_a.vcf

 

grep "^#" test.vcf > keep/test_b.vcf

grep "chr.*PASS" test.vcf >> keep/test_b.vcf

diff keep/test_a.vcf keep/test_b.vcf

I'm able to load a test VCF named "02.vcf" on my machine; that may or may not turn out to be the issue.

-Jacob

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Jacob Silterra
Software Engineer
Broad Institute