Problem With Gene Product Name Generator (Ahrd)?

Question

[Venky]

Hi All,

I am trying to retrieve product names for the proteins in my genome. For this i am using the tool AHRD (https://github.com/groupschoof/AHRD), i would like to know if someone has used this tool before. I am currently encountering a Java error due to the possibly issues with the blastparser in the program, has anyone else faced the same issue?

Query: "java -Xmx2g -jar ./dist/ahrd.jar genome.yml"

Error: "Started AHRD...

...initialised proteins in 0sec, currently occupying 5 MB We are sorry, an un-expected ERROR occurred: java.lang.NullPointerException at org.biojava.bio.program.sax.BlastSAXParser.interpret(BlastSAXParser.java:224) at org.biojava.bio.program.sax.BlastSAXParser.parse(BlastSAXParser.java:168) at org.biojava.bio.program.sax.BlastLikeSAXParser.onNewDataSet(BlastLikeSAXParser.java:314) at org.biojava.bio.program.sax.BlastLikeSAXParser.interpret(BlastLikeSAXParser.java:276) at org.biojava.bio.program.sax.BlastLikeSAXParser.parse(BlastLikeSAXParser.java:163) at ahrd.model.BlastResult.parseBlastResults(Unknown Source) at ahrd.controller.AHRD.parseBlastResults(Unknown Source) at ahrd.controller.AHRD.setup(Unknown Source) at ahrd.controller.AHRD.main(Unknown Source)"

Any help is appreciated! Also, does anybody have suggestions for better product name generating tools?

Thanks

[393099545m]

Hi Venky, do you solve your problem ? I am using this tool to name my proteins but the program always stop at beginning.Leave the massage : '... initialised proteins in 0sec, currently occupying 181M ' on the screen and don't go on any more . I cant find any error ....

Any help is appreciated. thank you .

[jomaco]

Hi, did you have any luck with this? I am encountering the same problem

Answer 1

[jomaco]

Did you use BLAST+ to produce the pairwise input files? (i.e. blastp)

I have found that when using blastall pairwise results (i.e. blastall -p blastp) I do not encounter this problem.