Hi , I am not familiar with Java, could you help me please with this kind of error?
my command:
java -jar -Xmx100G pilon-1.23.jar --genome genome.fasta --frags /illumina-data/Minimap_for_Pilon/Pilon/alg.sorted.bam --outdir /home1/tdanis/illumina-data/Minimap_for_Pilon/Pilon --output pilon1 --fix all --changes --verbose --threads 32
and after 1 hour running...
Exception in thread "main" java.io.FileNotFoundException: /home1/illumina-data/Minimap_for_Pilon/Pilon/home1/illumina-data/Minimap_for_Pilon/Pilon/pilon1.changes (No such file or directory)
at java.io.FileOutputStream.open0(Native Method)
at java.io.FileOutputStream.open(FileOutputStream.java:270)
at java.io.FileOutputStream.(FileOutputStream.java:213)
at java.io.FileOutputStream.(FileOutputStream.java:162)
at java.io.FileWriter.(FileWriter.java:90)
at org.broadinstitute.pilon.GenomeFile.processRegions(GenomeFile.scala:131)
at org.broadinstitute.pilon.Pilon$.main(Pilon.scala:105)
at org.broadinstitute.pilon.Pilon.main(Pilon.scala)
Hi , I am not familiar with Java, could you help me please with this kind of error? my command: java -jar -Xmx100G pilon-1.23.jar --genome genome.fasta --frags /illumina-data/Minimap_for_Pilon/Pilon/alg.sorted.bam --outdir /home1/tdanis/illumina-data/Minimap_for_Pilon/Pilon --output pilon1 --fix all --changes --verbose --threads 32
and after 1 hour running...
Exception in thread "main" java.io.FileNotFoundException: /home1/illumina-data/Minimap_for_Pilon/Pilon/home1/illumina-data/Minimap_for_Pilon/Pilon/pilon1.changes (No such file or directory) at java.io.FileOutputStream.open0(Native Method) at java.io.FileOutputStream.open(FileOutputStream.java:270) at java.io.FileOutputStream.(FileOutputStream.java:213)
at java.io.FileOutputStream.(FileOutputStream.java:162)
at java.io.FileWriter.(FileWriter.java:90)
at org.broadinstitute.pilon.GenomeFile.processRegions(GenomeFile.scala:131)
at org.broadinstitute.pilon.Pilon$.main(Pilon.scala:105)
at org.broadinstitute.pilon.Pilon.main(Pilon.scala)