Open RPHdejongh opened 6 years ago
cmd: "java -jar git_imports/pantools/dist/pantools.jar add_annotations -dp /tmp/jongh020/treu2013_pangenome -af gff_files.txt"
gff file that caused the crash: /mnt/scratch/jongh020/P3/treu2013/ncbi-genomes-2018-01-12/PRJEA37863_EC1118/PRJEA37863_EC1118_genomic.gff
output: ------------------------------- PanTools ------------------------------ Indexing 12871034 kmers... genome genes mRNAs tRNAs rRNAs 1 6074 5222 234 0 2 6079 4767 225 0 3 5268 4400 221 0 4 6026 5045 213 0 5 3294 3129 0 0 6 6361 6351 270 21 Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 3 at pangenome.AnnotationLayer.parse_gff(AnnotationLayer.java:269) at pangenome.AnnotationLayer.add_annotaions(AnnotationLayer.java:213) at pantools.Pantools.main(Pantools.java:252)
Possible reason for crash is gff file contains sequence information.
cmd: "java -jar git_imports/pantools/dist/pantools.jar add_annotations -dp /tmp/jongh020/treu2013_pangenome -af gff_files.txt"
gff file that caused the crash: /mnt/scratch/jongh020/P3/treu2013/ncbi-genomes-2018-01-12/PRJEA37863_EC1118/PRJEA37863_EC1118_genomic.gff
output: ------------------------------- PanTools ------------------------------ Indexing 12871034 kmers... genome genes mRNAs tRNAs rRNAs 1 6074 5222 234 0 2 6079 4767 225 0 3 5268 4400 221 0 4 6026 5045 213 0 5 3294 3129 0 0 6 6361 6351 270 21 Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 3 at pangenome.AnnotationLayer.parse_gff(AnnotationLayer.java:269) at pangenome.AnnotationLayer.add_annotaions(AnnotationLayer.java:213) at pantools.Pantools.main(Pantools.java:252)
Possible reason for crash is gff file contains sequence information.