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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 is running but no .changes file in output #166

Closed NicMAlexandre closed 3 months ago

NicMAlexandre commented 8 months ago

Hello,

Ive been running a loop using the following structure:

java -Xmx500G -jar pilon-1.24.jar --genome ${GENOME} --unpaired ${GENOME%.fasta}.sorted.bam --output ${GENOME%.fasta} --outdir Genome/ --changes --fix all --threads 20 --diploid

I am getting output fasta files as well as a log file (designated with slurm) suggesting Pilon is running and making corrections, but after each run there is no changes file documenting what was done.