======================================================================
ALIGN lean: reads -> own purged assembly
======================================================================
[align] bc2041 -> own assembly (m84082_250614_081210_s3.hifi_reads.demux.bc2041--bc2041.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_250614_081210_s3.hifi_reads.demux.bc2041--bc2041.bam' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2041.to_own.sorted.bam'
  $ '/usr/bin/samtools' index '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2041.to_own.sorted.bam'
  $ '/usr/bin/samtools' flagstat '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2041.to_own.sorted.bam' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2041.flagstat.txt'
[align] bc2068 -> own assembly (m84082_251001_025627_s2.hifi_reads.bc2068.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.bc2068.bam' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2068.to_own.sorted.bam'
  $ '/usr/bin/samtools' index '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2068.to_own.sorted.bam'
  $ '/usr/bin/samtools' flagstat '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2068.to_own.sorted.bam' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2068.flagstat.txt'
[align] bc2069 -> own assembly (m84082_250614_101514_s4.hifi_reads.demux.bc2069--bc2069.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_250614_101514_s4.hifi_reads.demux.bc2069--bc2069.bam' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2069.to_own.sorted.bam'
  $ '/usr/bin/samtools' index '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2069.to_own.sorted.bam'
  $ '/usr/bin/samtools' flagstat '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2069.to_own.sorted.bam' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2069.flagstat.txt'
[align] bc2070 -> own assembly (m84082_250614_101514_s4.hifi_reads.demux.bc2070--bc2070.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_250614_101514_s4.hifi_reads.demux.bc2070--bc2070.bam' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2070.to_own.sorted.bam'
  $ '/usr/bin/samtools' index '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2070.to_own.sorted.bam'
  $ '/usr/bin/samtools' flagstat '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2070.to_own.sorted.bam' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2070.flagstat.txt'
======================================================================
ALIGN siscowet: reads -> own purged assembly
======================================================================
[align] bc2071 -> own assembly (m84082_250614_081210_s3.hifi_reads.demux.bc2071--bc2071.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/siscowet.purged.mmi' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/data/pacbio-reads/m84082_250614_081210_s3.hifi_reads.demux.bc2071--bc2071.bam' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2071.to_own.sorted.bam'
  $ '/usr/bin/samtools' index '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2071.to_own.sorted.bam'
  $ '/usr/bin/samtools' flagstat '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2071.to_own.sorted.bam' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2071.flagstat.txt'
[align] bc2072 -> own assembly (m84082_250614_081210_s3.hifi_reads.demux.bc2072--bc2072.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/siscowet.purged.mmi' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/data/pacbio-reads/m84082_250614_081210_s3.hifi_reads.demux.bc2072--bc2072.bam' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2072.to_own.sorted.bam'
  $ '/usr/bin/samtools' index '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2072.to_own.sorted.bam'
  $ '/usr/bin/samtools' flagstat '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2072.to_own.sorted.bam' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2072.flagstat.txt'
[align] bc2073 -> own assembly (m84082_250614_101514_s4.hifi_reads.demux.bc2073--bc2073.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/siscowet.purged.mmi' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/data/pacbio-reads/m84082_250614_101514_s4.hifi_reads.demux.bc2073--bc2073.bam' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2073.to_own.sorted.bam'
  $ '/usr/bin/samtools' index '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2073.to_own.sorted.bam'
  $ '/usr/bin/samtools' flagstat '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2073.to_own.sorted.bam' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2073.flagstat.txt'
[align] bc2096 -> own assembly (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/siscowet.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-native-methylation/align/bc2096.to_own.sorted.bam'
  $ '/usr/bin/samtools' index '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2096.to_own.sorted.bam'
  $ '/usr/bin/samtools' flagstat '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2096.to_own.sorted.bam' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2096.flagstat.txt'
  $ '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/code/04-pacbio/tools/modkit' pileup '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2041.to_own.sorted.bam' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2041.CpG.bedmethyl' --cpg --combine-strands --ref '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/output/21.1-gene-anchored-synteny/lean.purged.fa' --threads 38
  $ awk -v OFS='\t' -v m=10 '$4=="m" && $10>=m{print $1,$2,$3,$11}' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2041.CpG.bedmethyl' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2041.cov10.bedGraph'
  $ awk -v OFS='\t' -v m=10 '$4=="m" && $10>=m{print $1,$2,$3,$12,$10}' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2041.CpG.bedmethyl' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2041.cpg_counts.bed'
  [bc2041] CpGs with cov>=10: 10,983,811
  $ '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/code/04-pacbio/tools/modkit' pileup '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2068.to_own.sorted.bam' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2068.CpG.bedmethyl' --cpg --combine-strands --ref '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/output/21.1-gene-anchored-synteny/lean.purged.fa' --threads 38
  $ awk -v OFS='\t' -v m=10 '$4=="m" && $10>=m{print $1,$2,$3,$11}' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2068.CpG.bedmethyl' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2068.cov10.bedGraph'
  $ awk -v OFS='\t' -v m=10 '$4=="m" && $10>=m{print $1,$2,$3,$12,$10}' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2068.CpG.bedmethyl' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2068.cpg_counts.bed'
  [bc2068] CpGs with cov>=10: 2,477,305
  $ '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/code/04-pacbio/tools/modkit' pileup '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2069.to_own.sorted.bam' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2069.CpG.bedmethyl' --cpg --combine-strands --ref '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/output/21.1-gene-anchored-synteny/lean.purged.fa' --threads 38
  $ awk -v OFS='\t' -v m=10 '$4=="m" && $10>=m{print $1,$2,$3,$11}' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2069.CpG.bedmethyl' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2069.cov10.bedGraph'
  $ awk -v OFS='\t' -v m=10 '$4=="m" && $10>=m{print $1,$2,$3,$12,$10}' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2069.CpG.bedmethyl' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2069.cpg_counts.bed'
  [bc2069] CpGs with cov>=10: 675,843
  $ '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/code/04-pacbio/tools/modkit' pileup '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2070.to_own.sorted.bam' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2070.CpG.bedmethyl' --cpg --combine-strands --ref '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/output/21.1-gene-anchored-synteny/lean.purged.fa' --threads 38
  $ awk -v OFS='\t' -v m=10 '$4=="m" && $10>=m{print $1,$2,$3,$11}' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2070.CpG.bedmethyl' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2070.cov10.bedGraph'
  $ awk -v OFS='\t' -v m=10 '$4=="m" && $10>=m{print $1,$2,$3,$12,$10}' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2070.CpG.bedmethyl' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2070.cpg_counts.bed'
  [bc2070] CpGs with cov>=10: 6,464,615
  $ '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/code/04-pacbio/tools/modkit' pileup '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2071.to_own.sorted.bam' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2071.CpG.bedmethyl' --cpg --combine-strands --ref '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/output/21.1-gene-anchored-synteny/siscowet.purged.fa' --threads 38
  $ awk -v OFS='\t' -v m=10 '$4=="m" && $10>=m{print $1,$2,$3,$11}' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2071.CpG.bedmethyl' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2071.cov10.bedGraph'
  $ awk -v OFS='\t' -v m=10 '$4=="m" && $10>=m{print $1,$2,$3,$12,$10}' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2071.CpG.bedmethyl' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2071.cpg_counts.bed'
  [bc2071] CpGs with cov>=10: 8,191,835
  $ '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/code/04-pacbio/tools/modkit' pileup '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2072.to_own.sorted.bam' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2072.CpG.bedmethyl' --cpg --combine-strands --ref '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/output/21.1-gene-anchored-synteny/siscowet.purged.fa' --threads 38
  $ awk -v OFS='\t' -v m=10 '$4=="m" && $10>=m{print $1,$2,$3,$11}' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2072.CpG.bedmethyl' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2072.cov10.bedGraph'
  $ awk -v OFS='\t' -v m=10 '$4=="m" && $10>=m{print $1,$2,$3,$12,$10}' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2072.CpG.bedmethyl' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2072.cpg_counts.bed'
  [bc2072] CpGs with cov>=10: 2,729,243
  $ '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/code/04-pacbio/tools/modkit' pileup '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2073.to_own.sorted.bam' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2073.CpG.bedmethyl' --cpg --combine-strands --ref '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/output/21.1-gene-anchored-synteny/siscowet.purged.fa' --threads 38
  $ awk -v OFS='\t' -v m=10 '$4=="m" && $10>=m{print $1,$2,$3,$11}' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2073.CpG.bedmethyl' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2073.cov10.bedGraph'
  $ awk -v OFS='\t' -v m=10 '$4=="m" && $10>=m{print $1,$2,$3,$12,$10}' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2073.CpG.bedmethyl' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2073.cpg_counts.bed'
  [bc2073] CpGs with cov>=10: 12,463,545
  $ '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/code/04-pacbio/tools/modkit' pileup '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/align/bc2096.to_own.sorted.bam' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2096.CpG.bedmethyl' --cpg --combine-strands --ref '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/output/21.1-gene-anchored-synteny/siscowet.purged.fa' --threads 38
  $ awk -v OFS='\t' -v m=10 '$4=="m" && $10>=m{print $1,$2,$3,$11}' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2096.CpG.bedmethyl' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2096.cov10.bedGraph'
  $ awk -v OFS='\t' -v m=10 '$4=="m" && $10>=m{print $1,$2,$3,$12,$10}' '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2096.CpG.bedmethyl' > '/home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/meth/bc2096.cpg_counts.bed'
  [bc2096] CpGs with cov>=10: 27,089,738

Done. Summary -> /home/shared/16TB_HDD_01/sr320/github/project-lake-trout/analyses/23-native-methylation/native_meth_summary.csv
Next: python3 code/23.9-native-meth-dmg.py