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PriceCollectSufficientStatistic error: Index 51 out of bounds for length 51 #19

Open dougbarrows opened 3 weeks ago

dougbarrows commented 3 weeks ago

Hello!

I am trying to run the PRICE workflow on a bam file. I've indexed the genome used to do the alignment and I get the error below when running the following command: 'gedi -e Price -D -reads test_sorted.bam -genomic ensembl_mm10_rm_primary -prefix test_out'.

I have also converted the bam file to a .cit file and I get the same error. Any thoughts you have would be greatly appreciated - thank you!

Std out:

2024-09-04 15:11:30.132 INFO OS: Linux 3.10.0-1127.el7.x86_64 amd64 2024-09-04 15:11:30.189 INFO Java: OpenJDK 64-Bit Server VM 11.0.23-internal+0-adhoc..src 2024-09-04 15:11:30.250 INFO Discovering classes in classpath 2024-09-04 15:11:30.432 INFO Preparing simple class references 2024-09-04 15:11:30.530 INFO Gedi version 1.0.6a (JAR) startup 2024-09-04 15:11:30.546 INFO Command: gedi -e Price -D -reads test_sorted.bam -genomic ensembl_mm10_rm_primary -prefix test_out 2024-09-04 15:11:30.546 INFO Price version 1.0.4 2024-09-04 15:11:30.718 INFO Reading oml /ru-auth/local/home/dbarrows/.gedi/genomic/ensembl_mm10_rm_primary.oml 2024-09-04 15:11:30.724 INFO Done reading oml /ru-auth/local/home/dbarrows/.gedi/genomic/ensembl_mm10_rm_primary.oml 2024-09-04 15:11:31.745 INFO Starting PriceIdentifyMaxPos ... 2024-09-04 15:11:31.745 INFO Starting PriceSetupOrfInference ... 2024-09-04 15:11:31.745 INFO Starting PriceClusterReads ... 2024-09-04 15:11:31.745 INFO Starting PriceCollectSufficientStatistics ... 2024-09-04 15:11:31.748 INFO Estimating maxpos... 2024-09-04 15:11:31.752 INFO Clustering reads 2024-09-04 15:11:32.165 INFO Finished PriceSetupOrfInference (time: 418ms) PRICE PRICE is an analysis method for Ribo-seq data.

Error: java.lang.RuntimeException: Could not run gedi.riboseq.javapipeline.PriceCollectSufficientStatistics@3248c902 Could not run gedi.riboseq.javapipeline.PriceCollectSufficientStatistics@3248c902 Index 51 out of bounds for length 51

gedi -e PRICE

General: -reads The mapped reads from the ribo-seq experiment. -prefix The prefix used for all output files -genomic The indexed GEDI genome.

Commandline: -progress Show progress -D Verbose output of errors -h Show usage -hh Show verbose usage -hhh Show extra verbose usage -dry Dry run -keep Do not remove temp files -changelog Show version changelog

java.lang.RuntimeException: java.lang.RuntimeException: Could not run gedi.riboseq.javapipeline.PriceCollectSufficientStatistics@3248c902 at gedi.util.job.schedule.DefaultPetriNetScheduler.run(DefaultPetriNetScheduler.java:222) at gedi.util.program.GediProgram$1.execute(GediProgram.java:403) at gedi.util.program.GediProgram.run(GediProgram.java:235) at executables.Price.main(Price.java:53) Caused by: java.lang.RuntimeException: Could not run gedi.riboseq.javapipeline.PriceCollectSufficientStatistics@3248c902 at gedi.util.program.GediProgramJob.execute(GediProgramJob.java:48) at gedi.util.program.GediProgramJob.execute(GediProgramJob.java:9) at gedi.util.job.FireTransition.call(FireTransition.java:37) at gedi.util.job.FireTransition.call(FireTransition.java:8) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.ArrayIndexOutOfBoundsException: Index 51 out of bounds for length 51 at gedi.riboseq.cleavage.CleavageModelEstimator.collectEstimateData(CleavageModelEstimator.java:367) at gedi.riboseq.javapipeline.PriceCollectSufficientStatistics.execute(PriceCollectSufficientStatistics.java:46) at gedi.util.program.GediProgramJob.execute(GediProgramJob.java:45) ... 7 more 2024-09-04 15:11:33.816 INFO Finished: gedi -e Price -D -reads test_sorted.bam -genomic ensembl_mm10_rm_primary -prefix test_out