needMem error in GBiB

[Xing Yin]

Dear all,


I'm trying to upload a big VCF file (1.3G)  to GBiB and I obtained the following error:

needMem: trying to allocate 1335182542 bytes (limit: 500000000)


Is there a way to bypass the limit?

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Thanks very much and best wishes,
Xing

[Brian Lee]

Dear Xing,

Thank you for using the UCSC Genome Browser in a Box (GBiB) and your question about the needMem error.

It sounds like you may be trying to upload the raw VCF file in text format, when you could build an index of the file and then point the Browser to the location of that indexed file and the original file (where they both have nearly exactly the same names). When indexed with an additional .tbi file, only the portions of the 1.3G file that you wish to display will be accessed, where the .tbi file will point the browser to where to find the data to pull out.

To build an index file for your VCF you will want to acquire tabix and bgzip and follow steps here: http://genome.ucsc.edu/goldenPath/help/vcf.html

Then you can put those two files, the 1.3G file and the related .tbi index file either in an internet accessible location, or share a local drive on your GBiB to your computer. Please have a look at our help documentation (http://genome.ucsc.edu/goldenPath/help/gbib.html) and the "Viewing Your Own Data" section (http://genome.ucsc.edu/goldenPath/help/gbib.html#YourTracks), for details on how to upload and view your own tracks. With your GBiB sharing a file you can quickly get the link to it from the "My Data" "GBiB Shared Data Folder" option. By copying that link you can paste the resulting link such as http://127.0.0.1:1234/folders/vcfExample.vcf.gz into the custom tracks page being sure the accompanying .tbi file exists there as well (vcfExample.vcf.gz.tbi, for example), and your track should display.

Thank you again for your inquiry and using the UCSC Genome Browser in a Box. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee
UC Santa Cruz Genomics Institute

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[Xing Yin]

Dear Brian,

Thanks! I followed the instructions and the problem is solved now!

Best wishes,
Xing