Hi Guys,
I’m a problem during the process of the conversion with maf2daa. In step 3 of the pipeline, an error occurs that I cannot resolve. I have increased the number of files that can be opened on the system (ulimit -n 1000000), but the error persists. Can someone help me?
Mistake:
java.io.FileNotFoundException: /data/tmp/bc1011.flye.dgpinheiro.nr.daa (Too many open files)
at java.io.RandomAccessFile.open0 (Native Method)
at java.io.RandomAccessFile.open (RandomAccessFile.java:316)
at java.io.RandomAccessFile. (RandomAccessFile.java:243)
at daa.writer.DAA_Writer.writeByteInFile (DAA_Writer.java:300)
at daa.writer.DAA_Writer.writeEnd (DAA_Writer.java:291)
at maf.MAF_StreamConverter.run (MAF_StreamConverter.java:123)
at startUp.MainConverter.main (MainConverter.java:175)
Command Line:
cat /data/michelligf/pacbio/MEGAN-LR/bc1011.flye.nr.maf | /data/bioinfo/megan6/tools/maf2daa -r /data/michelligf/pacbio/flye-assembly/bc1011/assembly.fasta -p 30 -cs 100m -t /data/tmp/ -o /data/tmp/bc1011.flye.dgpinheiro.nr.daa