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Sheikhizadeh / pantools

PanTools
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Multiple Add operations fail #5

Open mwhitesi opened 7 years ago

mwhitesi commented 7 years ago

Hi,

I have been unable to call the add operation more than once. The first time is successful, but then on the second call, it fails. E.g.

java -Xmx8g -jar /home/matt/pantools/dist/pantools.jar build $DBPATH $INPUTFILE 31 ... works ok java -Xmx8g -jar /home/matt/pantools/dist/pantools.jar add $DBPATH $INPUTFILE2 ... works ok java -Xmx8g -jar /home/matt/pantools/dist/pantools.jar add $DBPATH $INPUTFILE3

Gives the following error output:

------------------------------- PanTools ------------------------------- Reading 5 genome(s)... Sequence 8/8 of genome 11 : /media/poolhouse/workspace/l_amr/data/load_test/fasta/10.fasta
Sequence 8/8 of genome 12 : /media/poolhouse/workspace/l_amr/data/load_test/fasta/11.fasta
Sequence 8/8 of genome 13 : /media/poolhouse/workspace/l_amr/data/load_test/fasta/12.fasta
Sequence 8/8 of genome 14 : /media/poolhouse/workspace/l_amr/data/load_test/fasta/13.fasta
Sequence 8/8 of genome 15 : /media/poolhouse/workspace/l_amr/data/load_test/fasta/14.fasta
/media/poolhouse/workspace/l_amr/data/load_test/db/databases/index.db/old_index Failed to make index!

If I delete the old_index directory and try again, I get this error:

------------------------------- PanTools ------------------------------- Reading 5 genome(s)... Sequence 12/12 of genome 16 : /media/poolhouse/workspace/l_amr/data/load_test/fasta/15.fasta
Sequence 12/12 of genome 17 : /media/poolhouse/workspace/l_amr/data/load_test/fasta/16.fasta
Sequence 12/12 of genome 18 : /media/poolhouse/workspace/l_amr/data/load_test/fasta/17.fasta
Sequence 12/12 of genome 19 : /media/poolhouse/workspace/l_amr/data/load_test/fasta/18.fasta
Sequence 12/12 of genome 20 : /media/poolhouse/workspace/l_amr/data/load_test/fasta/19.fasta
Indexing 52053215 kmers...
Running KMC2...
75767740 new kmers generated.
Updating kmer index...
Exception in thread "main" java.lang.IndexOutOfBoundsException at java.nio.Buffer.checkIndex(Buffer.java:546) at java.nio.DirectByteBuffer.putLong(DirectByteBuffer.java:806) at index.IndexDatabase.put_pointer(IndexDatabase.java:511) at index.IndexDatabase.(IndexDatabase.java:356) at pangenome.SequenceLayer.add(SequenceLayer.java:213) at pantools.Pantools.main(Pantools.java:137)

thanks for your help.

matt

Sheikhizadeh commented 7 years ago

Thank you Matt for letting me know. I sorted it out.