Exception in thread "pool-1-thread-1" ...

[khuntco]

Received the following error after running the follow job:

java -jar aptasuite-0.9.2.jar -parse -predict -trace -config

Exception in thread "pool-1-thread-1" java.lang.NullPointerException           
    at lib.parser.aptaplex.FastqReader.getNextRead(FastqReader.java:126)
    at lib.parser.aptaplex.AptaPlexProducer.run(AptaPlexProducer.java:180)
    at java.lang.Thread.run(Thread.java:745)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)

[drivenbyentropy]

Hi,

Have you provided a configuration file after the -config parameter? If not, please have a look in the wiki as to how to create it for your experiment.

[khuntco]

Sorry I should have specified that I do have a config and a path to the config.cfg file.

This occurs after successful initialization and specifically occurs during the AptaPlexParser run

log_2018-10-09_12-42-37.txt

config.cfg.txt

[drivenbyentropy]

Thanks for the clarification. It looks to me that the NullPointerException might be occurring when reading the last read of the fastq file. Based on the number of total reads, would you be able to verify this for me?

I will then see if I can reproduce this issue locally.

Thanks!

[khuntco]

Thanks for the clarification. It looks to me that the NullPointerException might be occurring when reading the last read of the fastq file. Based on the number of total reads, would you be able to verify this for me?

I went to verify my last round .fastq file and sure enough it had been altered and damaged. After fixing this issue, AptaplexParser completed with no faults.

Thanks for your help.

[drivenbyentropy]

Great! Glad the issue got solved.