====================================================================== DIRECTION lean reads -> siscowet assembly ====================================================================== [align] bc2041->siscowet exists, skipping [align] bc2068->siscowet exists, skipping [align] bc2069->siscowet exists, skipping [align] bc2070->siscowet exists, skipping $ sort -k1,1 -k2,2n '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2041.to_siscowet.absent_merged.bed' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2041.to_siscowet.absent_merged.bed.srt' $ sort -k1,1 -k2,2n '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2068.to_siscowet.absent_merged.bed' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2068.to_siscowet.absent_merged.bed.srt' $ sort -k1,1 -k2,2n '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2069.to_siscowet.absent_merged.bed' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2069.to_siscowet.absent_merged.bed.srt' $ sort -k1,1 -k2,2n '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2070.to_siscowet.absent_merged.bed' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2070.to_siscowet.absent_merged.bed.srt' $ '/usr/bin/bedtools' multiinter -i '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2041.to_siscowet.absent_merged.bed.srt' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2068.to_siscowet.absent_merged.bed.srt' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2069.to_siscowet.absent_merged.bed.srt' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2070.to_siscowet.absent_merged.bed.srt' | awk -v OFS='\t' '$4>=4{print $1,$2,$3}' | '/usr/bin/bedtools' merge -i - > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/lean_reads_on_siscowet.absent_all4.bed' $ sort -k1,1 -k2,2n '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2041.to_siscowet.present_merged.bed' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2041.to_siscowet.present_merged.bed.srt' $ sort -k1,1 -k2,2n '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2068.to_siscowet.present_merged.bed' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2068.to_siscowet.present_merged.bed.srt' $ sort -k1,1 -k2,2n '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2069.to_siscowet.present_merged.bed' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2069.to_siscowet.present_merged.bed.srt' $ sort -k1,1 -k2,2n '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2070.to_siscowet.present_merged.bed' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2070.to_siscowet.present_merged.bed.srt' $ '/usr/bin/bedtools' multiinter -i '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2041.to_siscowet.present_merged.bed.srt' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2068.to_siscowet.present_merged.bed.srt' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2069.to_siscowet.present_merged.bed.srt' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2070.to_siscowet.present_merged.bed.srt' | awk -v OFS='\t' '$4>=4{print $1,$2,$3}' | '/usr/bin/bedtools' merge -i - > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/lean_reads_on_siscowet.present_all4.bed' $ awk -v OFS='\t' '($3-$2)>=1000{print $1,$2,$3,"a"NR}' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/lean_reads_on_siscowet.absent_all4.bed' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/siscowet_specific.present_regions.on_siscowet.bed.named' $ '/usr/bin/bedtools' flank -i '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/siscowet_specific.present_regions.on_siscowet.bed.named' -g '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/siscowet.chrom.sizes' -l 2000 -r 0 > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/siscowet_specific.present_regions.on_siscowet.bed.lf' $ '/usr/bin/bedtools' flank -i '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/siscowet_specific.present_regions.on_siscowet.bed.named' -g '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/siscowet.chrom.sizes' -l 0 -r 2000 > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/siscowet_specific.present_regions.on_siscowet.bed.rf' $ '/usr/bin/bedtools' intersect -a '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/siscowet_specific.present_regions.on_siscowet.bed.lf' -b '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/lean_reads_on_siscowet.present_all4.bed' -u | cut -f4 | sort -u > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/siscowet_specific.present_regions.on_siscowet.bed.ls' $ '/usr/bin/bedtools' intersect -a '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/siscowet_specific.present_regions.on_siscowet.bed.rf' -b '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/lean_reads_on_siscowet.present_all4.bed' -u | cut -f4 | sort -u > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/siscowet_specific.present_regions.on_siscowet.bed.rs' $ comm -12 '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/siscowet_specific.present_regions.on_siscowet.bed.ls' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/siscowet_specific.present_regions.on_siscowet.bed.rs' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/siscowet_specific.present_regions.on_siscowet.bed.both' $ awk 'NR==FNR{k[$1]=1;next} ($4 in k)' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/siscowet_specific.present_regions.on_siscowet.bed.both' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/siscowet_specific.present_regions.on_siscowet.bed.named' | cut -f1-3 | sort -k1,1 -k2,2n > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/siscowet_specific.present_regions.on_siscowet.bed' $ sort -k1,1 -k2,2n '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/lean_specific.novel_seq.on_siscowet.bed.tagged' | '/usr/bin/bedtools' merge -i - -d 100 -c 4 -o count_distinct,distinct | awk -v OFS='\t' '$4>=3{print $1,$2,$3,$5}' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/lean_specific.novel_seq.on_siscowet.bed' $ '/usr/bin/bedtools' intersect -a '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/output/21.1-gene-anchored-synteny/siscowet.purged.liftoff.genes.bed' -b '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/siscowet_specific.present_regions.on_siscowet.bed' -u | sort -k1,1 -k2,2n > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/siscowet_specific.genes.tsv.tmp' [siscowet-specific present] regions=340 bp=697,000 genes=71 [lean-specific novel] clusters=115,171 bp=10,269,719 ====================================================================== DIRECTION siscowet reads -> lean assembly ====================================================================== [align] bc2071->lean exists, skipping [align] bc2072->lean exists, skipping [align] bc2073->lean exists, skipping [align] bc2096 -> lean (m84082_251001_025627_s2.hifi_reads.bc2096.bam) $ '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/code/04-pacbio/tools/pbmm2' align --preset CCS --sort -j 46 '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/align/lean.purged.mmi' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/data/pacbio-reads/m84082_251001_025627_s2.hifi_reads.bc2096.bam' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/align/bc2096.to_lean.sorted.bam' $ '/usr/bin/samtools' index '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/align/bc2096.to_lean.sorted.bam' $ '/usr/bin/samtools' flagstat '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/align/bc2096.to_lean.sorted.bam' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/align/bc2096.to_lean.flagstat.txt' $ '/home/sr320/miniconda3/envs/syri_env/bin/mosdepth' --threads 8 --no-per-base --by 1000 '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/cov/bc2096.to_lean' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/align/bc2096.to_lean.sorted.bam' $ zcat '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/cov/bc2096.to_lean.regions.bed.gz' | awk -v OFS='\t' '$4==0{print $1,$2,$3}' | '/usr/bin/bedtools' merge -i - > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2096.to_lean.absent_merged.bed' $ zcat '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/cov/bc2096.to_lean.regions.bed.gz' | awk -v OFS='\t' '$4>0{print $1,$2,$3}' | '/usr/bin/bedtools' merge -i - > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2096.to_lean.present_merged.bed' $ '/usr/bin/samtools' view '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/align/bc2096.to_lean.sorted.bam' | '/usr/bin/gawk' '{chrom=$3; if(chrom=="*")next; ref=$4; cig=$6; while(match(cig,/([0-9]+)([MIDNSHP=X])/,a)){len=a[1]+0; op=a[2]; if(op=="I"&&len>=50) print chrom"\t"ref"\t"ref+1"\tI\t"len > "/dev/stdout"; if(op=="D"&&len>=50) print chrom"\t"ref"\t"ref+len"\tD\t"len > "/dev/stderr"; if(op=="M"||op=="D"||op=="N"||op=="="||op=="X") ref+=len; cig=substr(cig,RSTART+RLENGTH)}}' 1> '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2096.to_lean.ins_raw.bed' 2> '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2096.to_lean.del_raw.bed' $ sort -k1,1 -k2,2n '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2096.to_lean.ins_raw.bed' | '/usr/bin/bedtools' merge -i - -c 4 -o count > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2096.to_lean.insertions.bed' $ sort -k1,1 -k2,2n '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2096.to_lean.del_raw.bed' | '/usr/bin/bedtools' merge -i - -c 4 -o count > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2096.to_lean.deletions.bed' $ sort -k1,1 -k2,2n '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2071.to_lean.absent_merged.bed' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2071.to_lean.absent_merged.bed.srt' $ sort -k1,1 -k2,2n '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2072.to_lean.absent_merged.bed' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2072.to_lean.absent_merged.bed.srt' $ sort -k1,1 -k2,2n '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2073.to_lean.absent_merged.bed' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2073.to_lean.absent_merged.bed.srt' $ sort -k1,1 -k2,2n '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2096.to_lean.absent_merged.bed' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2096.to_lean.absent_merged.bed.srt' $ '/usr/bin/bedtools' multiinter -i '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2071.to_lean.absent_merged.bed.srt' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2072.to_lean.absent_merged.bed.srt' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2073.to_lean.absent_merged.bed.srt' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2096.to_lean.absent_merged.bed.srt' | awk -v OFS='\t' '$4>=4{print $1,$2,$3}' | '/usr/bin/bedtools' merge -i - > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/siscowet_reads_on_lean.absent_all4.bed' $ sort -k1,1 -k2,2n '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2071.to_lean.present_merged.bed' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2071.to_lean.present_merged.bed.srt' $ sort -k1,1 -k2,2n '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2072.to_lean.present_merged.bed' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2072.to_lean.present_merged.bed.srt' $ sort -k1,1 -k2,2n '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2073.to_lean.present_merged.bed' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2073.to_lean.present_merged.bed.srt' $ sort -k1,1 -k2,2n '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2096.to_lean.present_merged.bed' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2096.to_lean.present_merged.bed.srt' $ '/usr/bin/bedtools' multiinter -i '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2071.to_lean.present_merged.bed.srt' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2072.to_lean.present_merged.bed.srt' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2073.to_lean.present_merged.bed.srt' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/bc2096.to_lean.present_merged.bed.srt' | awk -v OFS='\t' '$4>=4{print $1,$2,$3}' | '/usr/bin/bedtools' merge -i - > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/siscowet_reads_on_lean.present_all4.bed' $ awk -v OFS='\t' '($3-$2)>=1000{print $1,$2,$3,"a"NR}' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/siscowet_reads_on_lean.absent_all4.bed' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/lean_specific.present_regions.on_lean.bed.named' $ '/usr/bin/bedtools' flank -i '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/lean_specific.present_regions.on_lean.bed.named' -g '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/lean.chrom.sizes' -l 2000 -r 0 > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/lean_specific.present_regions.on_lean.bed.lf' $ '/usr/bin/bedtools' flank -i '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/lean_specific.present_regions.on_lean.bed.named' -g '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/lean.chrom.sizes' -l 0 -r 2000 > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/lean_specific.present_regions.on_lean.bed.rf' $ '/usr/bin/bedtools' intersect -a '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/lean_specific.present_regions.on_lean.bed.lf' -b '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/siscowet_reads_on_lean.present_all4.bed' -u | cut -f4 | sort -u > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/lean_specific.present_regions.on_lean.bed.ls' $ '/usr/bin/bedtools' intersect -a '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/lean_specific.present_regions.on_lean.bed.rf' -b '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/calls/siscowet_reads_on_lean.present_all4.bed' -u | cut -f4 | sort -u > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/lean_specific.present_regions.on_lean.bed.rs' $ comm -12 '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/lean_specific.present_regions.on_lean.bed.ls' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/lean_specific.present_regions.on_lean.bed.rs' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/lean_specific.present_regions.on_lean.bed.both' $ awk 'NR==FNR{k[$1]=1;next} ($4 in k)' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/lean_specific.present_regions.on_lean.bed.both' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/lean_specific.present_regions.on_lean.bed.named' | cut -f1-3 | sort -k1,1 -k2,2n > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/lean_specific.present_regions.on_lean.bed' $ sort -k1,1 -k2,2n '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/siscowet_specific.novel_seq.on_lean.bed.tagged' | '/usr/bin/bedtools' merge -i - -d 100 -c 4 -o count_distinct,distinct | awk -v OFS='\t' '$4>=3{print $1,$2,$3,$5}' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/siscowet_specific.novel_seq.on_lean.bed' $ '/usr/bin/bedtools' intersect -a '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/output/21.1-gene-anchored-synteny/lean.purged.liftoff.genes.bed' -b '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/lean_specific.present_regions.on_lean.bed' -u | sort -k1,1 -k2,2n > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/lean_specific.genes.tsv.tmp' [lean-specific present] regions=343 bp=870,000 genes=44 [siscowet-specific novel] clusters=175,748 bp=17,176,221 Done. Summary -> /home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-reciprocal-pav/reciprocal_pav_summary.csv