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, 10:54, 23 June 2015
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| ::#* gotcloud/bin/genomestrip.pl - you only need to update this one if you want to run genomestrip | | ::#* gotcloud/bin/genomestrip.pl - you only need to update this one if you want to run genomestrip |
| ::#* gotcloud/scripts/bed-diff.pl - you only need to update this one if you plan to run bed-diff.pl | | ::#* gotcloud/scripts/bed-diff.pl - you only need to update this one if you plan to run bed-diff.pl |
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| + | |
| + | == ldrefine Pipeline FAQs == |
| + | ; make<nowiki>: *** [outdir/beagle/chr#/split/bgl.#.chr#.PASS.#.vcf.gz.tbi] Error 1</nowiki> |
| + | : Check the log file at: <code>outdir/beagle/chr#/split/bgl.#.err</code> |
| + | : If it says: |
| + | :: '''Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: -2''' |
| + | ::: '''at phaser.j.a(Unknown Source)<br /> at phaser.j.c(Unknown Source)<br /> at phaser.h.a(Unknown Source)<br /> at phaser.E.a(Unknown Source)<br /> at phaser.Y.a(Unknown Source)<br /> at phaser.PhaseMain.<init>(Unknown Source)<br /> at phaser.PhaseMain.main(Unknown Source)''' |
| + | : You need to change the seed for running beagle. |
| + | :* In your configuration file, set: |
| + | :** <code>BEAGLE = java -Xmx4g -jar $(BIN_DIR)/beagle.20101226.jar seed=993470 gprobs=true niterations=50 lowmem=true</code> |
| + | :* If it fails again, change the seed in the above command to something else, and rerun. |
| | | |
| == Tutorial FAQs == | | == Tutorial FAQs == |