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broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool
GNU General Public License v2.0
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Exception in thread "main" #110

Closed Tdanis closed 3 years ago

Tdanis commented 4 years ago

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)

marce-sarrias commented 3 years ago

Hi Tdanis,

I'm having a similar issue. How did you fix it? Thanks!

Tdanis commented 3 years ago

Hello Marce-sarrias,

You could just re-run the job. After two effrots, it was OK. Thanks