### run hifiasm ##

start_time=$SECONDS

TOOLPATH=/grid/bsr/data/data/utama/tools/hifiasm/hifiasm
FILEPATH=/isilon/seq/smrt4/smrtlink/userdata/jobs_root/0000/0000000/0000000836/outputs/m54333U_220413_184611.hifi_reads.fastq.gz

OUTPREFIX='soy_zarir_benson_apr2022.asm'

## Use -f0 for small genomes and -f39 for larger than human genomes
${TOOLPATH} -o ${OUTPREFIX} -t32 --write-paf ${FILEPATH} 2> ${OUTPREFIX}.log
awk '/^S/{print ">"$2;print $3}' ${OUTPREFIX}.bp.p_ctg.gfa > ${OUTPREFIX}.p_ctg.fa  # get primary contigs in FASTA

elapsed=$(( SECONDS - start_time ))
eval "echo Elapsed time: $(date -ud "@$elapsed" +'$((%s/3600/24)) days %H hr %M min %S sec')"