batch file making igv snapshots sporadically fails to show data about igv HOT 2 CLOSED

This means I probably have not been successful in making batch runs single threaded.

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On Jul 23, 2012, at 10:21 AM, Jacob [email protected] wrote:

Hi

I've been trying to use igv batch scripts to create snapshots of several hundred somatic mutations from bam files with WES, whole WGS, and RNA-seq data. Occasionally the snapshots show only subsets of the the loaded data. There are no error messages indicating problems loading the data.
This error is not always reproducible, but examples of scripts and resulting snap shots of the same data are here:

script (399 mutations, 2533 igv command lines):
http://iwww.broadinstitute.org/~stewart/EwingsSarcoma/review/AN_Sigma_EwingSarcoma_01Jun2012_22Jul2012.igv.commands.txt

example of correct display:
http://iwww.broadinstitute.org/~stewart/EwingsSarcoma/review/pix_AN_Sigma_EwingSarcoma_01Jun2012/EwngSRC-SJDES018-STAG2-chrX-123176418-Splice_Site-capture_wgs_rna_chrX_123176418.png

missing RNA-seq:
http://iwww.broadinstitute.org/~stewart/EwingsSarcoma/review/pix_AN_Sigma_EwingSarcoma_01Jun2012_20Jul2012/EwngSRC-SJDES018-STAG2-chrX-123176418-Splice_Site-capture_wgs_rna_chrX_123176418_C%3EA.png

missing RNA-seq and normal sample WGS data:
http://iwww.broadinstitute.org/~stewart/EwingsSarcoma/review/pix_AN_Sigma_EwingSarcoma_01Jun2012_22Jul2012/EwngSRC-SJDES018-STAG2-chrX-123176418-Splice_Site-capture_wgs_rna_chrX_123176418_C%3EA.png

In the script the missing data begins to occur with sample EwngSRC-SJDES007 mutation FAM21A chr10-51892644 Missense_Mutation and is intermittent.

I've tried igv with -Xmx750m and with -Xmx5750m without improvement one way or the other. Is there something wrong with the batch commands?

IGV Version 2.1.18 (2530)06/10/2012
linux: cga2.broadinstitute.org

Thanks,

Chip Stewart

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#8

from igv.

Loading data is typically asynchronous, I don't believe there is any synchronization done to wait for the data to load

from igv.