App-Anchr
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doc/model_organisms.md  view on Meta::CPAN 


    if [ ! -e R1.fq.gz ]; then
        echo >&2 '    R1.fq.gz not exists'
        exit;
    fi

    if [ -e pe.cor.fa ]; then
        echo >&2 '    pe.cor.fa exists'
        exit;
    fi

    if [[ {1} -ge '30' ]]; then
        anchr quorum \
            R1.fq.gz R2.fq.gz Rs.fq.gz \
            -p 16 \
            -o quorum.sh
    else
        anchr quorum \
            R1.fq.gz R2.fq.gz \
            -p 16 \
            -o quorum.sh
    fi

    bash quorum.sh
    
    echo >&2
    " ::: 20 25 30 35 ::: 60

# Stats of processed reads
bash ~/Scripts/cpan/App-Anchr/share/sr_stat.sh 1 header \
    > stat1.md

parallel -k --no-run-if-empty -j 3 "
    if [ ! -d 2_illumina/Q{1}L{2} ]; then
        exit;
    fi

    bash ~/Scripts/cpan/App-Anchr/share/sr_stat.sh 1 2_illumina/Q{1}L{2} ${REAL_G}
    " ::: 20 25 30 35 ::: 60 \
     >> stat1.md

cat stat1.md
```

| Name   | SumIn | CovIn | SumOut | CovOut | Discard% | AvgRead |  Kmer |  RealG |   EstG | Est/Real |   RunTime |
|:-------|------:|------:|-------:|-------:|---------:|--------:|------:|-------:|-------:|---------:|----------:|
| Q20L60 | 2.67G | 219.3 |  2.28G |  187.9 |  14.327% |     149 | "105" | 12.16M | 12.66M |     1.04 | 0:07'19'' |
| Q25L60 |  2.5G | 205.9 |   2.2G |  181.2 |  11.967% |     149 | "105" | 12.16M | 12.16M |     1.00 | 0:06'55'' |
| Q30L60 | 2.44G | 201.0 |  2.18G |  179.5 |  10.664% |     148 | "105" | 12.16M | 12.06M |     0.99 | 0:06'49'' |
| Q35L60 | 2.19G | 180.4 |  1.98G |  163.0 |   9.633% |     146 | "105" | 12.16M | 11.95M |     0.98 | 0:10'16'' |

* Clear intermediate files.

```bash
BASE_NAME=s288c
cd $HOME/data/anchr/${BASE_NAME}

find 2_illumina -type f -name "quorum_mer_db.jf" | xargs rm
find 2_illumina -type f -name "k_u_hash_0"       | xargs rm
find 2_illumina -type f -name "*.tmp"            | xargs rm
find 2_illumina -type f -name "pe.renamed.fastq" | xargs rm
find 2_illumina -type f -name "se.renamed.fastq" | xargs rm
find 2_illumina -type f -name "pe.cor.sub.fa"    | xargs rm
```

## s288c: down sampling

```bash
BASE_NAME=s288c
REAL_G=12157105
cd ${HOME}/data/anchr/${BASE_NAME}

for QxxLxx in $( parallel "echo 'Q{1}L{2}'" ::: 20 25 30 35 ::: 60 ); do
    echo "==> ${QxxLxx}"

    if [ ! -e 2_illumina/${QxxLxx}/pe.cor.fa ]; then
        echo "2_illumina/${QxxLxx}/pe.cor.fa not exists"
        continue;
    fi

    for X in 40 80 120 160; do
        printf "==> Coverage: %s\n" ${X}
        
        rm -fr 2_illumina/${QxxLxx}X${X}*
    
        faops split-about -l 0 \
            2_illumina/${QxxLxx}/pe.cor.fa \
            $(( ${REAL_G} * ${X} )) \
            "2_illumina/${QxxLxx}X${X}"
        
        MAX_SERIAL=$(
            cat 2_illumina/${QxxLxx}/environment.json \
                | jq ".SUM_OUT | tonumber | . / ${REAL_G} / ${X} | floor | . - 1"
        )
        
        for i in $( seq 0 1 ${MAX_SERIAL} ); do
            P=$( printf "%03d" ${i})
            printf "  * Part: %s\n" ${P}
            
            mkdir -p "2_illumina/${QxxLxx}X${X}P${P}"
            
            mv  "2_illumina/${QxxLxx}X${X}/${P}.fa" \
                "2_illumina/${QxxLxx}X${X}P${P}/pe.cor.fa"
            cp 2_illumina/${QxxLxx}/environment.json "2_illumina/${QxxLxx}X${X}P${P}"
    
        done
    done
done

```

## s288c: k-unitigs and anchors (sampled)

```bash
BASE_NAME=s288c
REAL_G=12157105
cd ${HOME}/data/anchr/${BASE_NAME}

# k-unitigs (sampled)
parallel --no-run-if-empty -j 1 "
    echo >&2 '==> Group Q{1}L{2}X{3}P{4}'

doc/model_organisms.md  view on Meta::CPAN 

platanus scaffold -t 16 \
    -c out_contig.fa -b out_contigBubble.fa \
    -ip1 pe.fa \
    2>&1 | tee sca_log.txt

platanus gap_close -t 16 \
    -c out_scaffold.fa \
    -ip1 pe.fa \
    2>&1 | tee gap_log.txt

```

## iso_1: quorum

```bash
BASE_NAME=iso_1
cd ${HOME}/data/anchr/${BASE_NAME}

parallel --no-run-if-empty -j 1 "
    cd 2_illumina/Q{1}L{2}
    echo >&2 '==> Group Q{1}L{2} <=='

    if [ ! -e R1.fq.gz ]; then
        echo >&2 '    R1.fq.gz not exists'
        exit;
    fi

    if [ -e pe.cor.fa ]; then
        echo >&2 '    pe.cor.fa exists'
        exit;
    fi

    if [[ {1} -ge '30' ]]; then
        anchr quorum \
            R1.fq.gz R2.fq.gz Rs.fq.gz \
            -p 16 \
            -o quorum.sh
    else
        anchr quorum \
            R1.fq.gz R2.fq.gz \
            -p 16 \
            -o quorum.sh
    fi

    bash quorum.sh
    
    echo >&2
    " ::: 20 25 30 ::: 60

```

Clear intermediate files.

```bash
BASE_NAME=iso_1
cd $HOME/data/anchr/${BASE_NAME}

find 2_illumina -type f -name "quorum_mer_db.jf" | xargs rm
find 2_illumina -type f -name "k_u_hash_0"       | xargs rm
find 2_illumina -type f -name "*.tmp"            | xargs rm
find 2_illumina -type f -name "pe.renamed.fastq" | xargs rm
find 2_illumina -type f -name "se.renamed.fastq" | xargs rm
find 2_illumina -type f -name "pe.cor.sub.fa"    | xargs rm
```

* Stats of processed reads

```bash
BASE_NAME=iso_1
cd ${HOME}/data/anchr/${BASE_NAME}

REAL_G=137567477

bash ~/Scripts/cpan/App-Anchr/share/sr_stat.sh 1 header \
    > stat1.md

parallel -k --no-run-if-empty -j 3 "
    if [ ! -d 2_illumina/Q{1}L{2} ]; then
        exit;
    fi

    bash ~/Scripts/cpan/App-Anchr/share/sr_stat.sh 1 2_illumina/Q{1}L{2} ${REAL_G}
    " ::: 20 25 30 ::: 60 \
     >> stat1.md

cat stat1.md
```

| Name   |  SumIn | CovIn | SumOut | CovOut | Discard% | AvgRead | Kmer |   RealG |    EstG | Est/Real |   RunTime |
|:-------|-------:|------:|-------:|-------:|---------:|--------:|-----:|--------:|--------:|---------:|----------:|
| Q20L60 | 15.65G | 113.7 | 13.86G |  100.8 |  11.383% |     100 | "71" | 137.57M |    129M |     0.94 | 1:02'31'' |
| Q25L60 | 14.66G | 106.5 | 13.26G |   96.4 |   9.506% |      99 | "71" | 137.57M | 127.11M |     0.92 | 0:58'16'' |
| Q30L60 |    14G | 101.7 | 12.97G |   94.3 |   7.364% |      99 | "71" | 137.57M |  126.4M |     0.92 | 0:56'23'' |

* kmergenie

```bash
BASE_NAME=iso_1
cd ${HOME}/data/anchr/${BASE_NAME}

mkdir -p 2_illumina/kmergenie
cd 2_illumina/kmergenie

kmergenie -l 21 -k 121 -s 10 -t 8 ../R1.fq.gz -o oriR1
kmergenie -l 21 -k 121 -s 10 -t 8 ../R2.fq.gz -o oriR2
kmergenie -l 21 -k 121 -s 10 -t 8 ../Q30L60/pe.cor.fa -o Q30L60

```

## iso_1: down sampling

```bash
BASE_NAME=iso_1
cd ${HOME}/data/anchr/${BASE_NAME}

REAL_G=137567477

for QxxLxx in $( parallel "echo 'Q{1}L{2}'" ::: 25 30 ::: 60 ); do
    echo "==> ${QxxLxx}"

    if [ ! -e 2_illumina/${QxxLxx}/pe.cor.fa ]; then
        echo "2_illumina/${QxxLxx}/pe.cor.fa not exists"

doc/model_organisms.md  view on Meta::CPAN 

    echo >&2 '==> Group Q{1}L{2} <=='

    if [ ! -e R1.fq.gz ]; then
        echo >&2 '    R1.fq.gz not exists'
        exit;
    fi

    if [ -e pe.cor.fa ]; then
        echo >&2 '    pe.cor.fa exists'
        exit;
    fi

    if [[ {1} -ge '30' ]]; then
        anchr quorum \
            R1.fq.gz R2.fq.gz Rs.fq.gz \
            -p 16 \
            -o quorum.sh
    else
        anchr quorum \
            R1.fq.gz R2.fq.gz \
            -p 16 \
            -o quorum.sh
    fi

    bash quorum.sh
    
    echo >&2
    " ::: 20 25 30 ::: 60

# Stats of processed reads
bash ~/Scripts/cpan/App-Anchr/share/sr_stat.sh 1 header \
    > stat1.md

parallel -k --no-run-if-empty -j 3 "
    if [ ! -d 2_illumina/Q{1}L{2} ]; then
        exit;
    fi

    bash ~/Scripts/cpan/App-Anchr/share/sr_stat.sh 1 2_illumina/Q{1}L{2} ${REAL_G}
    " ::: 20 25 30 ::: 60 \
     >> stat1.md

cat stat1.md
```

| Name   |  SumIn | CovIn | SumOut | CovOut | Discard% | AvgRead | Kmer |   RealG |   EstG | Est/Real |   RunTime |
|:-------|-------:|------:|-------:|-------:|---------:|--------:|-----:|--------:|-------:|---------:|----------:|
| Q20L60 | 10.55G | 105.2 |  6.37G |   63.5 |  39.659% |      99 | "71" | 100.29M | 99.05M |     0.99 | 0:54'45'' |
| Q25L60 |  9.88G |  98.5 |  6.38G |   63.6 |  35.443% |      97 | "71" | 100.29M | 98.89M |     0.99 | 0:53'22'' |
| Q30L60 |  8.88G |  88.5 |  7.42G |   73.9 |  16.455% |      91 | "69" | 100.29M | 98.82M |     0.99 | 0:51'43'' |

* Clear intermediate files.

```bash
BASE_NAME=n2
cd $HOME/data/anchr/${BASE_NAME}

find 2_illumina -type f -name "quorum_mer_db.jf" | xargs rm
find 2_illumina -type f -name "k_u_hash_0"       | xargs rm
find 2_illumina -type f -name "*.tmp"            | xargs rm
find 2_illumina -type f -name "pe.renamed.fastq" | xargs rm
find 2_illumina -type f -name "se.renamed.fastq" | xargs rm
find 2_illumina -type f -name "pe.cor.sub.fa"    | xargs rm
```

* kmergenie

```bash
BASE_NAME=n2
cd ${HOME}/data/anchr/${BASE_NAME}

mkdir -p 2_illumina/kmergenie
cd 2_illumina/kmergenie

kmergenie -l 21 -k 91 -s 10 -t 8 ../R1.fq.gz -o oriR1
kmergenie -l 21 -k 91 -s 10 -t 8 ../R2.fq.gz -o oriR2
kmergenie -l 21 -k 91 -s 10 -t 8 ../Q30L60/pe.cor.fa -o Q30L60

```

## n2: down sampling

```bash
BASE_NAME=n2
REAL_G=100286401
cd ${HOME}/data/anchr/${BASE_NAME}

for QxxLxx in $( parallel "echo 'Q{1}L{2}'" ::: 25 30 ::: 60 ); do
    echo "==> ${QxxLxx}"

    if [ ! -e 2_illumina/${QxxLxx}/pe.cor.fa ]; then
        echo "2_illumina/${QxxLxx}/pe.cor.fa not exists"
        continue;
    fi

    for X in 30 60; do
        printf "==> Coverage: %s\n" ${X}
        
        rm -fr 2_illumina/${QxxLxx}X${X}*
    
        faops split-about -l 0 \
            2_illumina/${QxxLxx}/pe.cor.fa \
            $(( ${REAL_G} * ${X} )) \
            "2_illumina/${QxxLxx}X${X}"
        
        MAX_SERIAL=$(
            cat 2_illumina/${QxxLxx}/environment.json \
                | jq ".SUM_OUT | tonumber | . / ${REAL_G} / ${X} | floor | . - 1"
        )
        
        for i in $( seq 0 1 ${MAX_SERIAL} ); do
            P=$( printf "%03d" ${i})
            printf "  * Part: %s\n" ${P}
            
            mkdir -p "2_illumina/${QxxLxx}X${X}P${P}"
            
            mv  "2_illumina/${QxxLxx}X${X}/${P}.fa" \
                "2_illumina/${QxxLxx}X${X}P${P}/pe.cor.fa"
            cp 2_illumina/${QxxLxx}/environment.json "2_illumina/${QxxLxx}X${X}P${P}"
    
        done
    done

doc/model_organisms.md  view on Meta::CPAN 

    echo >&2 '==> Group Q{1}L{2} <=='

    if [ ! -e R1.fq.gz ]; then
        echo >&2 '    R1.fq.gz not exists'
        exit;
    fi

    if [ -e pe.cor.fa ]; then
        echo >&2 '    pe.cor.fa exists'
        exit;
    fi

    if [[ {1} -ge '30' ]]; then
        anchr quorum \
            R1.fq.gz R2.fq.gz Rs.fq.gz \
            -p 16 \
            -o quorum.sh
    else
        anchr quorum \
            R1.fq.gz R2.fq.gz \
            -p 16 \
            -o quorum.sh
    fi

    bash quorum.sh
    
    echo >&2
    " ::: 20 25 30 ::: 60

# Stats of processed reads
bash ~/Scripts/cpan/App-Anchr/share/sr_stat.sh 1 header \
    > stat1.md

parallel -k --no-run-if-empty -j 3 "
    if [ ! -d 2_illumina/Q{1}L{2} ]; then
        exit;
    fi

    bash ~/Scripts/cpan/App-Anchr/share/sr_stat.sh 1 2_illumina/Q{1}L{2} ${REAL_G}
    " ::: 20 25 30 ::: 60 \
     >> stat1.md

cat stat1.md
```

| Name   |  SumIn | CovIn | SumOut | CovOut | Discard% | AvgRead |  Kmer |   RealG |    EstG | Est/Real |   RunTime |
|:-------|-------:|------:|-------:|-------:|---------:|--------:|------:|--------:|--------:|---------:|----------:|
| Q20L60 | 13.36G | 111.6 |  7.48G |   62.5 |  43.986% |     254 | "127" | 119.67M | 131.52M |     1.10 | 1:03'05'' |
| Q25L60 | 11.82G |  98.8 |  8.43G |   70.4 |  28.710% |     236 | "127" | 119.67M | 125.44M |     1.05 | 0:56'14'' |
| Q30L60 | 10.37G |  86.7 |  8.73G |   73.0 |  15.807% |     218 | "127" | 119.67M | 119.21M |     1.00 | 0:49'53'' |

* Clear intermediate files.

```bash
BASE_NAME=col_0
cd $HOME/data/anchr/${BASE_NAME}

find 2_illumina -type f -name "quorum_mer_db.jf" | xargs rm
find 2_illumina -type f -name "k_u_hash_0"       | xargs rm
find 2_illumina -type f -name "*.tmp"            | xargs rm
find 2_illumina -type f -name "pe.renamed.fastq" | xargs rm
find 2_illumina -type f -name "se.renamed.fastq" | xargs rm
find 2_illumina -type f -name "pe.cor.sub.fa"    | xargs rm
```

* kmergenie

```bash
BASE_NAME=col_0
cd ${HOME}/data/anchr/${BASE_NAME}

mkdir -p 2_illumina/kmergenie
cd 2_illumina/kmergenie

kmergenie -l 21 -k 91 -s 10 -t 8 ../Q30L60/pe.cor.fa -o Q30L60

```

## col_0: down sampling

```bash
BASE_NAME=col_0
REAL_G=119667750
cd ${HOME}/data/anchr/${BASE_NAME}

for QxxLxx in $( parallel "echo 'Q{1}L{2}'" ::: 25 30 ::: 60 ); do
    echo "==> ${QxxLxx}"

    if [ ! -e 2_illumina/${QxxLxx}/pe.cor.fa ]; then
        echo "2_illumina/${QxxLxx}/pe.cor.fa not exists"
        continue;
    fi

    for X in 30 60; do
        printf "==> Coverage: %s\n" ${X}
        
        rm -fr 2_illumina/${QxxLxx}X${X}*
    
        faops split-about -l 0 \
            2_illumina/${QxxLxx}/pe.cor.fa \
            $(( ${REAL_G} * ${X} )) \
            "2_illumina/${QxxLxx}X${X}"
        
        MAX_SERIAL=$(
            cat 2_illumina/${QxxLxx}/environment.json \
                | jq ".SUM_OUT | tonumber | . / ${REAL_G} / ${X} | floor | . - 1"
        )
        
        for i in $( seq 0 1 ${MAX_SERIAL} ); do
            P=$( printf "%03d" ${i})
            printf "  * Part: %s\n" ${P}
            
            mkdir -p "2_illumina/${QxxLxx}X${X}P${P}"
            
            mv  "2_illumina/${QxxLxx}X${X}/${P}.fa" \
                "2_illumina/${QxxLxx}X${X}P${P}/pe.cor.fa"
            cp 2_illumina/${QxxLxx}/environment.json "2_illumina/${QxxLxx}X${X}P${P}"
    
        done
    done
done



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