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gifford-lab / GEM3

GEM software suite (GEM, GPS, KMAC, KSM, RMD, etc.)
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Error running GEM #8

Open JMFZ opened 5 years ago

JMFZ commented 5 years ago

Hello, After running several GEM jobs I received the following error and stops running:

IP: 16932832 Ctrl: 16296675 IP/Ctrl: 1,04

Sorting reads and selecting enriched regions ... java.lang.ArrayIndexOutOfBoundsException: -1 at edu.mit.csail.cgs.deepseq.discovery.KPPMixture.calcSlope(KPPMixture.java:3078) at edu.mit.csail.cgs.deepseq.discovery.KPPMixture.getSlope(KPPMixture.java:3057) at edu.mit.csail.cgs.deepseq.discovery.KPPMixture.calcIpCtrlRatio(KPPMixture.java:1995) at edu.mit.csail.cgs.deepseq.discovery.KPPMixture.(KPPMixture.java:360) at edu.mit.csail.cgs.deepseq.discovery.GEM.(GEM.java:146) at edu.mit.csail.cgs.deepseq.discovery.GEM.main(GEM.java:343) Exception in thread "main" java.lang.NullPointerException at edu.mit.csail.cgs.deepseq.discovery.GEM.runMixtureModel(GEM.java:166) at edu.mit.csail.cgs.deepseq.discovery.GEM.main(GEM.java:345)

I must say that I got this error while running with two particular BAMs but not with some other BAMs using the same command, since with the latter I got nice data. I’d appreciate any advice. Regards,

yguoma commented 5 years ago

Please post your command line arguments for running GEM with the error datasets. You might also want to convert them into BED files first, and then run GEM.

Best,

Yuchun

On Fri, Sep 28, 2018 at 1:20 PM JMFZ notifications@github.com wrote:

Hello, After running several GEM jobs I received the following error and stops running:

IP: 16932832 Ctrl: 16296675 IP/Ctrl: 1,04

Sorting reads and selecting enriched regions ... java.lang.ArrayIndexOutOfBoundsException: -1 at edu.mit.csail.cgs.deepseq.discovery.KPPMixture.calcSlope(KPPMixture.java:3078) at edu.mit.csail.cgs.deepseq.discovery.KPPMixture.getSlope(KPPMixture.java:3057) at edu.mit.csail.cgs.deepseq.discovery.KPPMixture.calcIpCtrlRatio(KPPMixture.java:1995) at edu.mit.csail.cgs.deepseq.discovery.KPPMixture.(KPPMixture.java:360) at edu.mit.csail.cgs.deepseq.discovery.GEM.(GEM.java:146) at edu.mit.csail.cgs.deepseq.discovery.GEM.main(GEM.java:343) Exception in thread "main" java.lang.NullPointerException at edu.mit.csail.cgs.deepseq.discovery.GEM.runMixtureModel(GEM.java:166) at edu.mit.csail.cgs.deepseq.discovery.GEM.main(GEM.java:345)

I must say that I got this error while running with two particular BAMs but not with some other BAMs using the same command, since with the latter I got nice data. I’d appreciate any advice. Regards,

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JMFZ commented 5 years ago

Thank you for your comments. Following you suggestions, I converted my BAMs into BED and got the same error. I guess there is no a problem with my command line since the same arguments don't give any error with some other BAMs.

My command line is:

java -Xmx4G -jar gem.jar --d Read_Distribution_default.txt --g TAIR10-genome_sizes.txt --genome ./AthGenome/ --s 120000000 --expt myBAMexp.bam --ctrl myBAMcont.bam --out myBAM-GEM --f BED --outNP --range 150 --smooth 4 --mrc 1 --fold 2 --q 1.301029996 --k_min 6 --k_max 20 --k_seqs 600 --k_neg_dinu_shuffle --pp_nmotifs 3

Many thanks for your interest Best,

Jose