search

njdbickhart / RAPTR-SV

RAPTR-SV uses Read Pair and Split Read methods to identify structural variants in paired-end WGS data
10 stars 3 forks source link

problem loading java #1

Open rajanikanthnmsu opened 9 years ago

rajanikanthnmsu commented 9 years ago

Dear Derek, I am Raj, and trying to use your program. I am getting some problem in loading. could you please check below and see what might be the problem.

[ spru@/scratch/ragovindarajulu/sorg_intraspecific_reads/bamfiles ] $ java -jar /shared/software/genomics/RAPTR-SV-0.0.15/store/RAPTR-SV.jar preprocess -i b35.sam.bam.sorted.bam -o b35rap -r Sorbi1_assembly_scaffolds_hardmasked.fasta -g -d [MAIN] Command line arguments supplied: preprocess -i b35.sam.bam.sorted.bam -o b35rap -r Sorbi1_assembly_scaffolds_hardmasked.fasta -g -d [MAIN] Debug flag set to: true [MAIN] RAPTR-SV version: 0.0.15 [MAIN] RAPTR-SV preprocess mode selected. Exception in thread "main" java.lang.NullPointerException at workers.BamMetadataGeneration.ScanFile(BamMetadataGeneration.java:107) at modes.PreprocessMode.run(PreprocessMode.java:91) at workers.RPSRmain.main(RPSRmain.java:69

njdbickhart commented 9 years ago

Hello Raj,

As we discussed, there was an issue with the readgroup lines in the BAM. I'm going to keep this issue open so that I improve the core program with better exception handling for cases like this.

Thanks, Derek