HI, I have been using Pilon to polish a fly genome assembly. I set the Kmer size to 29, but still exceeds the haashmap table max, which is 2147483648. I gave the comand 700G RAM. Fly genome size is about 800MB.
error i get:
Exception in thread "main" java.lang.RuntimeException: new HashMap table size -2147483648 exceeds maximum
Can I set the new hashmap table size, compiling, how ? any ideas?
thanks!
HI, I have been using Pilon to polish a fly genome assembly. I set the Kmer size to 29, but still exceeds the haashmap table max, which is 2147483648. I gave the comand 700G RAM. Fly genome size is about 800MB. error i get: Exception in thread "main" java.lang.RuntimeException: new HashMap table size -2147483648 exceeds maximum
Can I set the new hashmap table size, compiling, how ? any ideas? thanks!
My command: java -Xmx200G -jar /shared/software/src/pilon/pilon-1.24.jar --genome /shared/workarea01/Anastrepha_fr_Genome2022/assemblyMale1_flye/assembly.fasta --frags maleMGI_flye1_sort.bam --output maleMGIpilon --changes --fix gaps,local,bases,breaks,novel --verbose