Open cmaggior opened 4 years ago
Hi!
I'm having the same issue as above
My input:
pilon -Xmx1400G --genome myassembly.fa --bam myassembly.mybarcodedreads.bam --changes --vcf --diploid --threads 35 --verbose --output myassembly_polished.fa
I'm running the job interactively and I see that the program is doing something correctly: `#fixBreak: 394826:3660-4064 L=1 R=1 S=0
L=1 R=1 S=0
L=2 R=1`
But i have no output files
did you solve the problem? I'm having the same issue!
No, I never did :/
did you solve the problem? I'm having the same issue!
I tried to trouble shooting it for two days now, finally figured out the problem i have. Remember that available system memory also plays a role, so ensure that the allocated memory does not exceed the physical memory available on your machine to avoid swapping and performance degradation.
So as i have a 32G ram laptop, i had to change -Xmx50G to -Xmx32G to be able to get the output file.
Hello,
I'm using Pilon to polish a metagenome with the following input:
java -jar $EBROOTPILON/pilon-1.23.jar --genome contigs_500.fasta --bam S1.sorted.bam --output pilon_1pair.fa
However no output file is generated, nor a log file. Can anyone please advise?