Rma2info NullPointerException

User Questions
1

Hi,

I am receiving a NullPointerException when running rma2info -r2c but not when doing rma2info -c2c after malt-run. Here is the error trace, I am running with a synonyms file. I discovered that 1 taxon in my reference was not present in taxonomy.map and taxonomy.tre, and after adding it to those files, I still receive the error. Thank you for your help! Let me know if there is any additional info that would be useful.

java.lang.NullPointerException
	at megan/megan.tools.RMA2Info.isDescendant(RMA2Info.java:455)
	at megan/megan.tools.RMA2Info.reportRead2Count(RMA2Info.java:387)
	at megan/megan.tools.RMA2Info.run(RMA2Info.java:153)
	at megan/megan.tools.RMA2Info.main(RMA2Info.java:63)
2

Hello, following up because this is a blocking issue:

I understand that this occurs becuase taxonomy.getANode(taxid) (line 455 of RMA2Info.java) returns Null. However, I cannot add print statements to see which taxId is causing this error, and all taxids in my database are present in the file taxonomy.map.

Does the .rma file store a mapping of reads to taxids? This is what I would like to retrieve.

3

Figured this out, in case anyone encounters. rma2info wasn’t using the same ncbi.map as in the malt database. I copied the ncbi.map file from the index to the directory in which I was running rma2info which fixed this issue.

4

I have modified the code so that it would throw an exception…