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ucl-pathgenomics / HaROLD

Haplotype Reconstruction of Longitudinal Deep sequencing data
MIT License
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Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 300000 out of bounds for length 300000 #6

Open npdungca opened 1 year ago

npdungca commented 1 year ago

This is the command line I ran with your simulated dataset: sample1_touse.strandcount.csv

[nina]$ h=1
[nina]$ cat $temp_dir/$convertedPrefx".txt"
sample1_touse.strandcount.csv
[nina]$ 
[nina]$ time java -jar $app_dir/jar/Cluster_RG/dist/HaROLD-2.0.jar         --count-file $temp_dir/$convertedPrefx".txt" --haplotypes ${h}         --alpha-frac 0.5 --gamma-cache 10000 --threads 32 -H -L -p $tempRes_prefix
Picked up JAVA_TOOL_OPTIONS: -Xmx2g
Picked up _JAVA_OPTIONS: -Xms256m -Xmx256g
Main: arguments = --count-file /scratch/nina7/SSenr9_harold/results/temp/BC32.converted.txt --haplotypes 1 --alpha-frac 0.5 --gamma-cache 10000 --threads 32 -H -L -p /scratch/nina7/SSenr9_harold/results/temp/BC3
2_H1_harold
Main: seed = 1714761951164
Optimisation method :BOBYQ
May 03, 2024 2:45:51 P.M. org.cache2k.core.Cache2kCoreProviderImpl
INFO: cache2k starting. version=1.0.2.Final, build=undefined, defaultImplementation=HeapCache
BC32.converted.txt: /scratch/nina7/SSenr9_harold/results/temp/BC32.converted.txt
BC32.converted.txt: haplotypes = 1
/scratch/nina7/SSenr9_harold/results/temp/BC32.converted.txt
initialFreqSet = false
/scratch/nina7/SSenr9_harold/results/temp/sample1_touse.strandcount.csv
Average read depth
0       81.90919980095208

[0]
BC32.converted.txt: timepoints = 1
BC32.converted.txt: sites = 227081
Starting pre-optimisation of hap frequencies, a = 0.99900000 0.03000000
[0.999, 0.03]
[1.0]
java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: Index 0 out of bounds for length 0
        at java.base/java.util.concurrent.FutureTask.report(FutureTask.java:122)
        at java.base/java.util.concurrent.FutureTask.get(FutureTask.java:191)
        at cluster_rg.Cluster_RG.getFutureResults(Cluster_RG.java:342)
        at cluster_rg.Cluster_RG.optimise(Cluster_RG.java:164)
        at cluster_rg.Cluster_RG.run(Cluster_RG.java:97)
        at cluster_rg.Cluster_RG.main(Cluster_RG.java:50)
Caused by: java.lang.ArrayIndexOutOfBoundsException: Index 0 out of bounds for length 0
        at cluster_rg.Cluster.run(Cluster.java:122)
        at cluster_rg.Cluster_RG.lambda$optimise$0(Cluster_RG.java:161)
        at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
        at java.base/java.lang.Thread.run(Thread.java:833)
Exception in thread "main" picocli.CommandLine$ExecutionException: Error
        at cluster_rg.Cluster_RG.run(Cluster_RG.java:123)
        at cluster_rg.Cluster_RG.main(Cluster_RG.java:50)
Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: Index 0 out of bounds for length 0
        at cluster_rg.Cluster_RG.getFutureResults(Cluster_RG.java:345)
        at cluster_rg.Cluster_RG.optimise(Cluster_RG.java:164)
        at cluster_rg.Cluster_RG.run(Cluster_RG.java:97)
        ... 1 more
Caused by: java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: Index 0 out of bounds for length 0
        at java.base/java.util.concurrent.FutureTask.report(FutureTask.java:122)
        at java.base/java.util.concurrent.FutureTask.get(FutureTask.java:191)
        at cluster_rg.Cluster_RG.getFutureResults(Cluster_RG.java:342)
        ... 3 more
Caused by: java.lang.ArrayIndexOutOfBoundsException: Index 0 out of bounds for length 0
        at cluster_rg.Cluster.run(Cluster.java:122)
        at cluster_rg.Cluster_RG.lambda$optimise$0(Cluster_RG.java:161)
        at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
        at java.base/java.lang.Thread.run(Thread.java:833)