Error AptamerPool backend using CLI on HPC

[xaimara-santiago]

Hi,

I'm really interested in using the program for my thesis project. I started using the GUI and was able to upload the data but clustering was taking to long and/or crashing, even though I was using just a couple of sequencing files at a time (files stored locally). Also, I was never able to successfully export the data or use it to open the experiment later on, so I had to start from zero every time. Right now I'm trying to use the CLI to run the program on a high performance computing facility (HPCf). For this, the sequencing files as well as configuration files for each experiment are stored at the HPCf system. When I try to run the -parse command the following error appears within seconds:

Instantiating MapDBAptamerPool Error invoking construtor of AptamerPool backend java.lang.reflect.InvocationTargetException at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at lib.aptamer.datastructures.Experiment.(Experiment.java:147) at aptasuite.CLI.createDatabase(CLI.java:305) at aptasuite.CLI.(CLI.java:145) at aptasuite.Aptasuite.main(Aptasuite.java:70) Caused by: org.mapdb.DBException$VolumeIOError at org.mapdb.volume.Volume.lockFile(Volume.java:498) at org.mapdb.volume.MappedFileVol.(MappedFileVol.java:88) at org.mapdb.volume.MappedFileVol$MappedFileFactory.factory(MappedFileVol.java:64) at org.mapdb.volume.MappedFileVol$MappedFileFactory.makeVolume(MappedFileVol.java:38) at org.mapdb.StoreDirect$volume$1.invoke(StoreDirect.kt:77) at org.mapdb.StoreDirect$volume$1.invoke(StoreDirect.kt:16) at org.mapdb.StoreDirect.(StoreDirect.kt:76) at org.mapdb.StoreDirect$Companion.make(StoreDirect.kt:57) at org.mapdb.StoreDirect$Companion.make$default(StoreDirect.kt:56) at org.mapdb.DBMaker$Maker.make(DBMaker.kt:450) at lib.aptamer.datastructures.MapDBAptamerPool.getMapDBInstance(MapDBAptamerPool.java:1116) at lib.aptamer.datastructures.MapDBAptamerPool.(MapDBAptamerPool.java:296) ... 8 more Caused by: java.io.IOException: Function not implemented at java.base/sun.nio.ch.FileDispatcherImpl.lock0(Native Method) at java.base/sun.nio.ch.FileDispatcherImpl.lock(FileDispatcherImpl.java:96) at java.base/sun.nio.ch.FileChannelImpl.tryLock(FileChannelImpl.java:1161) at java.base/java.nio.channels.FileChannel.tryLock(FileChannel.java:1165) at org.mapdb.volume.Volume.lockFile(Volume.java:490) ... 19 more

I would appreciate any help you could provide.