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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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Pilon Killed with no other error message #169

Open dorie8 opened 3 months ago

dorie8 commented 3 months ago

Hi, I have been using Pilon for a few genomes but recently ran into this problem. The job is killed with no other error message mid run. Here is my command: java -Xmx350G -jar pilon-1.24.jar --fix bases --genome scaffolds_FINAL.fasta --frags UnAln_combined.bam --output output --outdir outdir/ it will run at first but at the second scaffold Large collapsed region: scaffold_2:112852126-112867253 size 15128 Large collapsed region: scaffold_2:112876528-112891288 size 14761 Killed and the output directory is empty My bam file is 91G. I also tried running with -Xmx500G but the job is still killed Appreciate any inputs on this! Thanks in advance.

lissacruzs commented 2 months ago

Hi,

I don't know if it will work for you but I add --fix all to my command line and it worked.