---
# System prepended metadata

title: Plants submission on hold

---

# Plants submission on hold

- Auto-generated Table of Content
[ToC]

## 1. dcPolAvic1
### 1.1 dcPolAvic1 normal MBG 3001k with mito and chloro reads

```

mu2@tol-head1:/lustre/scratch116/tol/projects/darwin/data/dicots/Polygonum_aviculare/working/mito_chloro$ echo '/software/team311/mu2/mbg-noKbug/MBG/bin/MBG -k 3001 -w 250 -a 5 -u 150 -i MW411186.1.MW411186.fasta.BOTH.HiFiMapped.bam.fasta -o HiFiMapped.bam.filtered.3k.gfa -t 12' | bsub -n12 -q long -R"span[hosts=1] select[mem>55000] rusage[mem=55000]" -M55000 -P team311 -o mbg.%J -e er.mbg.%J
Job <688828> is submitted to queue <long>.
```

![](https://i.imgur.com/OmUrv0p.png)


OBS: I've ran MBG modified and other k sizes for this species. Other results are:
``` 
/lustre/scratch116/tol/projects/darwin/data/dicots/Polygonum_aviculare/working/mito_chloro
```

### 1.2

```
(biopython) mu2@tol-head1:/lustre/scratch123/tol/projects/darwin/data/dicots/Polygonum_aviculare/working/mito_chloro$ python /software/team311/mu2/join_segments.py HiFiMapped.bam.filtered.3k.fa chlro.path HiFiMapped.bam.filtered.3k.gfa chloro.fa
Collecting sequences from HiFiMapped.bam.filtered.3k.fa
Reading links from HiFiMapped.bam.filtered.3k.gfa
=======================================
Processing  1+,2+,3+,2-
1+ 2+
================== Basic step
1+ 2+ 4332M
From cigar 4332
Added coordinates: [96641 - 123226)
2+ 3+
================== Basic step
2+ 3+ 4587M
From cigar 4587
Added coordinates: [123226 - 141277)
3+ 2-
================== Basic step
3+ 2- 4587M
From cigar 4587
Added coordinates: [141277 - 167607)
Writing chloro

```
chloro 1+,2+,3+,2-


```
(biopython) mu2@tol-head1:/lustre/scratch123/tol/projects/darwin/data/dicots/Polygonum_aviculare/working/mito_chloro/mitohifi_chloro$ echo 'python  /software/team311/jf18/git_softwares/MitoHiFi_2/mitohifi-v3-fromCirc_v02.13.4.py -c chloro.fa -f NC_058892.1.fasta -g NC_058892.1.gb -o 11 -t 18  ' | bsub -n18 -q long -R"span[hosts=1] select[mem>98000] rusage[mem=98000]" -M98000 -P team311 -o prof.%J -e er.prof.%J 
Job <981728> is submitted to queue <long>.

```
![](https://i.imgur.com/bll3tR2.png)

### 1.2.1 Chloro sent for submission

```
/lustre/scratch123/tol/projects/darwin/data/dicots/Polygonum_aviculare/working/mito_chloro/mitohifi_chloro/potential_contigs/chloro/chloro.annotation/chloro.annotation_MitoFinder_mitfi_Final_Results
```

### 1.3 Mito

4.fa

```
(biopython) mu2@tol-head1:/lustre/scratch123/tol/projects/darwin/data/dicots/Polygonum_aviculare/working/mito_chloro/mitohifi_mito$ echo 'python  /software/team311/jf18/git_softwares/MitoHiFi_2/mitohifi-v3-fromCirc_v02.13.4.py -c 4.fa -f MW664926.1.fasta -g MW664926.1.gb -o 1 -t 18  ' | bsub -n18 -q long -R"span[hosts=1] select[mem>98000] rusage[mem=98000]" -M98000 -P team311 -o prof.%J -e er.prof.%J 
Job <981738> is submitted to queue <long>.
```


![](https://i.imgur.com/ebetnjT.png)


### 1.3.1 Mito sent for submission

```
 /lustre/scratch123/tol/projects/darwin/data/dicots/Polygonum_aviculare/working/mito_chloro/mitohifi_mito
 ```
 

## 2. drFilUlma1

### 2.1 modified k=3001

```
mu2@tol-head1:/lustre/scratch116/tol/projects/darwin/data/dicots/Filipendula_ulmaria/working/drFilUlma1.hifiasm.20210726/mito_chloro_modofied$ echo '/software/team311/mu2/mito_experiment_MBG/MBG/bin/MBG --output-sequence-paths 1001-modi-paths.gaf --resolve-maxk 10000 -k 3001 -w 250 -t 12 -a 2 -u 20 -i MK567782.1_MW464867.1.fasta.BOTH.HiFiMapped.bam.fasta -o modi3001-mbg.gfa ' | bsub -n12 -q long -R"span[hosts=1] select[mem>55000] rusage[mem=55000]" -M55000 -P team311 -o mbg.%J -e er.mbg.%J
Job <688935> is submitted to queue <long>.
```


![](https://i.imgur.com/yoJwZSG.png)


OBS: more runs at: 

```
/lustre/scratch116/tol/projects/darwin/data/dicots/Filipendula_ulmaria/working/drFilUlma1.hifiasm.20210726/mito_chloro_modofied
```

## 3. drPotAnse1

### 3.1 normal MBG k=1001

![](https://i.imgur.com/lmdi3Cl.png)


#### 3.1.1 Mitochondria

```
(biopython) mu2@tol-head1:/lustre/scratch124/tol/projects/darwin/data/dicots/Potentilla_anserina/working/mito_chloro$ python /software/team311/mu2/join_segments.py MT677853_MW464867.1.fasta.BOTH.HiFiMapped.bam.filtered.1k.fa mito1.path MT677853_MW464867.1.fasta.BOTH.HiFiMapped.bam.filtered.1k.gfa mito1.path.fa
Collecting sequences from MT677853_MW464867.1.fasta.BOTH.HiFiMapped.bam.filtered.1k.fa
Reading links from MT677853_MW464867.1.fasta.BOTH.HiFiMapped.bam.filtered.1k.gfa
=======================================
Processing  5+,6-,4+,6-
5+ 6-
================== Basic step
5+ 6- 1432M
From cigar 1432
Added coordinates: [191480 - 195265)
6- 4+
================== Basic step
6- 4+ 1393M
From cigar 1393
Added coordinates: [195265 - 292201)
4+ 6-
================== Basic step
4+ 6- 1432M
From cigar 1432
Added coordinates: [292201 - 295986)
Writing mito1
```


![](https://i.imgur.com/kT1lI9E.png)

```
/lustre/scratch123/tol/projects/darwin/data/dicots/Potentilla_anserina/working/mito_chloro/mitohifi_mito/final_mitogenome.annotation/final_mitogenome.annotation_MitoFinder_mitfi_Final_Results
```


#### 3.1.2 another mapping

![](https://i.imgur.com/Nr2oGsk.png)

#### 3.1.2.1 mito submitted to james

```
/lustre/scratch123/tol/projects/darwin/data/dicots/Potentilla_anserina/working/mito_chloro/mitohifi_mito/potential_contigs/mito1/mito1.annotation/mito1.annotation_MitoFinder_mitfi_Final_Results
```


### 3.1.2 Chloroplast
```
(biopython) mu2@tol-head1:/lustre/scratch124/tol/projects/darwin/data/dicots/Potentilla_anserina/working/mito_chloro$ python /software/team311/mu2/join_segments.py MT677853_MW464867.1.fasta.BOTH.HiFiMapped.bam.filtered.1k.fa chloro1.path MT677853_MW464867.1.fasta.BOTH.HiFiMapped.bam.filtered.1k.gfa chloro1.path.fa
Collecting sequences from MT677853_MW464867.1.fasta.BOTH.HiFiMapped.bam.filtered.1k.fa
Reading links from MT677853_MW464867.1.fasta.BOTH.HiFiMapped.bam.filtered.1k.gfa
=======================================
Processing  3+,2-,1+,2+
3+ 2-
================== Basic step
3+ 2- 1426M
From cigar 1426
Added coordinates: [87863 - 112385)
2- 1+
================== Basic step
2- 1+ 1451M
From cigar 1451
Added coordinates: [112385 - 132552)
1+ 2+
================== Basic step
1+ 2+ 1451M
From cigar 1451
Added coordinates: [132552 - 157049)
Writing chloro1
```
```
/lustre/scratch123/tol/projects/darwin/data/dicots/Potentilla_anserina/working/mito_chloro/mapping1
```

Chloro in correct order
![](https://i.imgur.com/T7F1D6h.png)

### 3.1.2.2 chloro submitted to James

```
/lustre/scratch123/tol/projects/darwin/data/dicots/Potentilla_anserina/working/mito_chloro/mitohifi_chloro/potential_contigs/chloro1/chloro1.annotation/chloro1.annotation_MitoFinder_mitfi_Final_Results
```


### 3.2 modified MBG k=3001


``` /software/team311/mu2/mito_experiment_MBG/MBG/bin/MBG --output-sequence-paths $ref.3001-modi-paths.gaf --resolve-maxk 10000 -k 3001 -w 250 -t 18 -a 2 -u 20 -i $ref.BOTH.HiFiMapped.bam.fasta -o $ref.modi3001-mbg.gfa ```

![](https://i.imgur.com/0fft5cU.png)



Obs: other runs

```/lustre/scratch116/tol/projects/darwin/data/dicots/Potentilla_anserina/working/mito_chloro/maptoboth2.sh ```



# 4. daLycEuro1

Segmentation fault

# 5. drAilAlti1
```
(biopython) mu2@tol-head2:/lustre/scratch116/tol/projects/darwin/data/dicots/Ailanthus_altissima/working/mito_chloro$ echo 'sh maptoboth2.sh ' | bsub -n18 -q normal -R"span[hosts=1] select[mem>75000] rusage[mem=75000]" -M75000 -P team311 -o mito.%J -e er.mito.%J
Job <832852> is submitted to queue <normal>.
```

## 5.1 k=5001

![](https://i.imgur.com/l8kB2Pi.png)


## 5.2 modified mbg k=3001

![](https://i.imgur.com/g6A2ilY.png)



# 6. drMedArab1
```
(biopython) mu2@tol-head2:/lustre/scratch116/tol/projects/darwin/data/dicots/Medicago_arabica/working/mito_chloro$ echo 'sh maptoboth2.sh ' | bsub -n18 -q normal -R"span[hosts=1] select[mem>75000] rusage[mem=75000]" -M75000 -P team311 -o mito.%J -e er.mito.%J
Job <833058> is submitted to queue <normal>.
```

## 6.1 k=5001

![](https://i.imgur.com/woWJdvE.png)



# 7. dhAlnGlut1
```
/lustre/scratch116/tol/projects/darwin/data/dicots/Alnus_glutinosa/working/mito_chloro
```
## 7.1 k=5001
![](https://i.imgur.com/rJ8MV9f.png)


# 8. daBalNigr1
```
(biopython) mu2@tol-head2:/lustre/scratch116/tol/projects/darwin/data/dicots/Ballota_nigra/working/mito_chloro$ echo 'sh maptoboth2.sh ' | bsub -n18 -q normal -R"span[hosts=1] select[mem>75000] rusage[mem=75000]" -M75000 -P team311 -o mbg.%J -e er.mbg.%J
Job <833181> is submitted to queue <normal>.
```
## 8.1. daBalNigr1 k=5001

```/lustre/scratch124/tol/projects/darwin/data/dicots/Ballota_nigra/working/mito_chloro ```



![](https://i.imgur.com/pBrGDfe.png)


### 8.1.1 mitochondria(s)

#### 8.1.1.2 daBalNigr1 MBG with all reads

![](https://i.imgur.com/c79pJ2X.png)



#### 8.1.1.2 5


![](https://i.imgur.com/4iKrFj5.png)


#### 8.1.1.3 4

![](https://i.imgur.com/ydOH6Ku.png)


### 8.1.2 chloroplast

```
(biopython) mu2@tol-head1:/lustre/scratch124/tol/projects/darwin/data/dicots/Ballota_nigra/working/mito_chloro$ python /software/team311/mu2/join_segments.py MK728874.1_MW338732.1.fasta.BOTH.HiFiMapped.bam.filtered.5k.fa chloro1.path MK728874.1_MW338732.1.fasta.BOTH.HiFiMapped.bam.filtered.5k.gfa chloro1.path.fa
Collecting sequences from MK728874.1_MW338732.1.fasta.BOTH.HiFiMapped.bam.filtered.5k.fa
Reading links from MK728874.1_MW338732.1.fasta.BOTH.HiFiMapped.bam.filtered.5k.gfa
=======================================
Processing  1+,2+,3+,2-
1+ 2+
================== Basic step
1+ 2+ 7151M
From cigar 7151
Added coordinates: [97376 - 115825)
2+ 3+
================== Basic step
2+ 3+ 7106M
From cigar 7106
Added coordinates: [115825 - 140570)
3+ 2-
================== Basic step
3+ 2- 7106M
From cigar 7106
Added coordinates: [140570 - 159064)
Writing chloro1

```

![](https://i.imgur.com/XYwYx4X.png)




## 8.2. daBalNigr1 modified k=3001

![](https://i.imgur.com/wyWlTLI.png)

## 8.3. modified k=1001



![](https://i.imgur.com/IjAiTW0.png)


## 8.4 More graphs with different parameters


```
MBG/bin/MBG -k 301 -w 150 -a 2 -u 70
```

![](https://i.imgur.com/EA7hCDV.png)


### 8.4.1 More graphs with different parameters

```
MBG -k 501 -w 150 -a 2 -u 70
```

![](https://i.imgur.com/NsMZTnD.png)


### 8.5 Graphs with all reads

Because the data shows mitochondria to be divided in at least 3 independent circles, I've ran several MBG runs with all the reads to see if its possible we might have missed at mito circlers hanging around.

#### 8.5.1  -k 1001 -w 250 -a 5 -u 150

k=1001, Window size of 250, minimum kmer abundance of 5, mininum unitig abundance of 150. Imagine bellow, we only see 3 circles again with the average coverage of ~900
![](https://i.imgur.com/BJk98yH.png)

#### 8.5.2  -k 5001 -w 250 -a 5 -u 150

k=5001, Window size of 250, minimum kmer abundance of 5, mininum unitig abundance of 150.

![](https://i.imgur.com/8VQRxFA.png)

Having a look at sequences:

```
mu2@tol-head2:/lustre/scratch124/tol/projects/darwin/data/dicots/Ballota_nigra/working/mito_chloro/mito_chloro_allReads$ python /software/team311/mu2/join_segments.py daBalNigr1.trimmedReads.fasta.5k.fa path daBalNigr1.trimmedReads.fasta.5k.gfa path.fa
Collecting sequences from daBalNigr1.trimmedReads.fasta.5k.fa
Reading links from daBalNigr1.trimmedReads.fasta.5k.gfa
=======================================
Processing  6+,7+,9+,4-,6+,5-,6+,7+,8+
6+ 7+
```

The 6,7,9 etc graph is ribossome

#### 8.5.3   --resolve-maxk 10000 -k 3001 -w 250  -a 2 -u 70

MBG modidied by Sergey k=3001, Window size of 250, minimum kmer abundance of 2, mininum unitig abundance of 70.

No more than the 3 circles in the graph bellow

![](https://i.imgur.com/9yxqu6x.png)


#### 8.5.4 --resolve-maxk 10000 -k 1001 -w 250 -a 2 -u 70

MBG modidied by Sergey k=1001, Window size of 250, minimum kmer abundance of 2, mininum unitig abundance of 70.

![](https://i.imgur.com/eWcF86r.jpg)

#### 8.5.5 -k 501 -w 150 -a 2 -u 70

k=501, Window size of 150, minimum kmer abundance of 2, mininum unitig abundance of 70
Even smaller kmers would only show the 3 circles

![](https://i.imgur.com/4aczqZ5.png)


### 8.5.6 Annotation 

![](https://i.imgur.com/EDuJ6ob.png)


# 9. drHedHeli1

```
(biopython) mu2@tol-head2:/lustre/scratch116/tol/projects/darwin/data/dicots/Hedera_helix/working/mito_chloro$ echo 'sh maptoboth2.sh' | bsub -n18 -q normal -R"span[hosts=1] select[mem>55000] rusage[mem=55000]" -M55000 -P team311 -o mbg.%J -e er.mbg.%J
Job <833245> is submitted to queue <normal>.
```
## 9.1. drHedHeli1 k=1001

![](https://i.imgur.com/e9oxdD6.png)

## 9.2. drHedHeli1 k=5001

![](https://i.imgur.com/rC3uHGu.png)


## 9.3. drHedHeli1 modified k=3001

![](https://i.imgur.com/Ks0QFHN.png)


# 10. drUrtUren1
```
(biopython) mu2@tol-head2:/lustre/scratch116/tol/projects/darwin/data/dicots/Urtica_urens/working/mito_chloro$ echo 'sh maptoboth2.sh' | bsub -n18 -q normal -R"span[hosts=1] select[mem>55000] rusage[mem=55000]" -M55000 -P team311 -o mbg.%J -e er.mbg.%J
Job <833293> is submitted to queue <normal>.
```
## 10.1. k=5001

![](https://i.imgur.com/OT8501F.png)

## 10.2. k=1001

![](https://i.imgur.com/3o5xRiQ.png)

## 10.3. modified k=3001

![](https://i.imgur.com/RCpAnMq.png)


    
# 11. daSolDulc1
```
(biopython) mu2@tol-head2:/lustre/scratch116/tol/projects/darwin/data/dicots/Solanum_dulcamara/working/mito_chloro$ echo 'sh maptoboth2.sh' | bsub -n18 -q normal -R"span[hosts=1] select[mem>55000] rusage[mem=55000]" -M55000 -P team311 -o mbg.%J -e er.mbg.%J
Job <833327> is submitted to queue <normal>.
```

## 11.1 daSolDulc1 k=1001

![](https://i.imgur.com/SjpRlH0.png)


## 11.2 daSolDulc1 k=5001

![](https://i.imgur.com/RGuNsDE.png)

## 11.3 daSolDulc1 modified k=3001

![](https://i.imgur.com/lBeHecU.png)


# 12. cbRhyLore1
```
(biopython) mu2@tol-head2:/lustre/scratch116/tol/projects/darwin/data/non-vascular-plants/Rhytidiadelphus_loreus/working/mito_chloroplast$ echo 'sh maptoboth2.sh' | bsub -n18 -q normal -R"span[hosts=1] select[mem>55000] rusage[mem=55000]" -M55000 -P team311 -o mbg.%J -e er.mbg.%J
Job <833461> is submitted to queue <normal>.
```
## 12.1. k=1001

![](https://i.imgur.com/JDdvj91.png)

## 12.2. k=5001

![](https://i.imgur.com/QY0vsez.png)


# 13. cbThuTama2

## 13.1 k=1001

![](https://i.imgur.com/8gUnL0g.png)

### 13.1.1 Mito

![](https://i.imgur.com/awzLyw1.png)


### 13.1.2 Chloro2
```
(blast12) mu2@tol-head1:/lustre/scratch123/tol/projects/darwin/data/non-vascular-plants/Thuidium_tamariscinum/working/mito_choro$ python /software/team311/mu2/join_segments.py NC_054351.1.MW429506.1.fasta.BOTH.HiFiMapped.bam.filtered.1k.fa path_chloro2 NC_054351.1.MW429506.1.fasta.BOTH.HiFiMapped.bam.filtered.1k.gfa path_chloro2.fa
Collecting sequences from NC_054351.1.MW429506.1.fasta.BOTH.HiFiMapped.bam.filtered.1k.fa
Reading links from NC_054351.1.MW429506.1.fasta.BOTH.HiFiMapped.bam.filtered.1k.gfa
=======================================
Processing  3+,2-,1+,2+
3+ 2-
================== Basic step
3+ 2- 1475M
From cigar 1475
Added coordinates: [90067 - 98291)
2- 1+
================== Basic step
2- 1+ 1513M
From cigar 1513
Added coordinates: [98291 - 118338)
1+ 2+
================== Basic step
1+ 2+ 1513M
From cigar 1513
Added coordinates: [118338 - 126524)
Writing chloro2
```

```
(biopython) mu2@tol-head1:/lustre/scratch123/tol/projects/darwin/data/non-vascular-plants/Thuidium_tamariscinum/working/mito_choro/mitohifi_chloro2$ echo 'python  /software/team311/jf18/git_softwares/MitoHiFi_2/mitohifi-v3-fromCirc_v02.13.4.py -c path_chloro2.fa -f MW429506.1.fasta  -g MW429506.1.gb -o 11 -t 16 -a plant ' | bsub -n16 -q long -R"span[hosts=1] select[mem>98000] rusage[mem=98000]" -M98000 -P team311 -o prof.%J -e er.prof.%J
Job <47567> is submitted to queue <long>.
```

![](https://i.imgur.com/mQKqc9V.png)



## 13.2 k=5001

![](https://i.imgur.com/9TEedp1.png)



# 14. drGeuUrba1
```
(biopython) mu2@tol-head2:/lustre/scratch116/tol/projects/darwin/data/dicots/Geum_urbanum/working/mito_chloro$ echo 'sh maptoboth2.sh' | bsub -n18 -q normal -R"span[hosts=1] select[mem>55000] rusage[mem=55000]" -M55000 -P team311 -o mbg.%J -e er.mbg.%J
Job <833707> is submitted to queue <normal>.
```

## 14.1 drGeuUrba1 k=1001

![](https://i.imgur.com/NITe6B6.png)

## 14.2 drGeuUrba1 k=5001

![](https://i.imgur.com/UXtRPGw.png)

## 14.3 drGeuUrba1 modified k=3001

![](https://i.imgur.com/CopA9bj.png)


# 15. lpJunEffu1
```
(biopython) mu2@tol-head2:/lustre/scratch116/tol/projects/darwin/data/monocots/Juncus_effusus/working/mito_chloro$ echo 'sh maptoboth2.sh' | bsub -n18 -q normal -R"span[hosts=1] select[mem>55000] rusage[mem=55000]" -M55000 -P team311 -o mbg.%J -e er.mbg.%J
Job <833762> is submitted to queue <normal>.
```

## 15.1 lpJunEffu1 k=1001

![](https://i.imgur.com/pv2mQxi.png)

## 15.2 lpJunEffu1 k=5001

![](https://i.imgur.com/VAQJ9WT.png)

## 15.3 lpJunEffu1 modified k=3001

![](https://i.imgur.com/YTbhAtG.png)


# 16. drChaAngu1
```
(biopython) mu2@tol-head2:/lustre/scratch116/tol/projects/darwin/data/dicots/Chamaenerion_angustifolium/working/mito_chloro$ echo 'sh maptoboth2.sh' | bsub -n18 -q normal -R"span[hosts=1] select[mem>55000] rusage[mem=55000]" -M55000 -P team311 -o mbg.%J -e er.mbg.%J
Job <833821> is submitted to queue <normal>.
```

## 16.1 drChaAngu1 k=1001

![](https://i.imgur.com/3sRjFpX.png)

## 16.2 drChaAngu1 k=5001

![](https://i.imgur.com/6OyTZvc.png)

## 16.3 drChaAngu1 modified k=1001

![](https://i.imgur.com/LRU0dr4.png)

## 16.4 drChaAngu1 modified k=3001

![](https://i.imgur.com/Z09FzM1.png)



# 17. daPulDyse1
```
(biopython) mu2@tol-head2:/lustre/scratch124/tol/projects/darwin/data/dicots/Pulicaria_dysenterica/working/mito_chloro$ echo 'sh maptoboth2.sh' | bsub -n18 -q normal -R"span[hosts=1] select[mem>55000] rusage[mem=55000]" -M55000 -P team311 -o mbg.%J -e er.mbg.%J
Job <833990> is submitted to queue <normal>.
```
## 17.1 daPulDyse1 k=1001

![](https://i.imgur.com/5hakBwH.png)


## 17.2 daPulDyse1 k=5001

![](https://i.imgur.com/xptdsol.png)

## 17.3 daPulDyse1 modified k=3001


![](https://i.imgur.com/mqfnEsW.png)


# 18. ddMerAnnu1 (being submitted for curation Feb 15th )

![](https://i.imgur.com/jNlhqHJ.png)


# 19. ddAraThal4

## 19.1. MBG k=1001

```/lustre/scratch124/tol/projects/darwin/data/dicots/Arabidopsis_thaliana/working/mito_chloro_mbg```

![](https://i.imgur.com/rlXAzfe.png)


### 19.1.1 Chloroplast by hand
```
biopython) mu2@tol-head2:/lustre/scratch124/tol/projects/darwin/data/dicots/Arabidopsis_thaliana/working/mito_chloro_mbg$ python /software/team311/mu2/join_segments.py NC_037304.1.MZ323108.1.fasta.BOTH.HiFiMapped.bam.filtered.1k.fa chloro.paths NC_037304.1.MZ323108.1.fasta.BOTH.HiFiMapped.bam.filtered.1k.gfa chloro.paths.joined.fasta
```

3+, 2-, 1-, 2+



Lucia says chloroplast orientation should be:

LSC-IR1-SSC-IR2 + making sure that the orientation of SSC is such that it ends with  ycf1


So what I did for now (on 19.1.) was:

SSC-IRb-LSC-IRa


# 20 drBuxSemp1

## 20.1 MBG  -k 2001 -w 250 -a 5 -u 150 


![](https://i.imgur.com/Tu8fsnG.png)


## 20.2 MBG  -k 3001 -w 250 -a 5 -u 150 

![](https://i.imgur.com/7YwXTVW.png)


### 20.2.1 Chloro
chloro 28+,27-,26+,27+

```
mu2@tol-head2:/lustre/scratch124/tol/projects/darwin/data/dicots/Buxus_sempervirens/working/mito_chloro$ python /software/team311/mu2/join_segments.py NC_058304.1.MZ934757.1.fasta.BOTH.HiFiMapped.bam.filtered.3k.fa chloro NC_058304.1.MZ934757.1.fasta.BOTH.HiFiMapped.bam.filtered.3k.gfa chloro.fa
Collecting sequences from NC_058304.1.MZ934757.1.fasta.BOTH.HiFiMapped.bam.filtered.3k.fa
Reading links from NC_058304.1.MZ934757.1.fasta.BOTH.HiFiMapped.bam.filtered.3k.gfa
=======================================
Processing  28+,27-,26+,27+
28+ 27-
================== Basic step
28+ 27- 4156M
From cigar 4156
Added coordinates: [104960 - 118671)
27- 26+
================== Basic step
27- 26+ 4283M
From cigar 4283
Added coordinates: [118671 - 141503)
26+ 27+
================== Basic step
26+ 27+ 4283M
From cigar 4283
Added coordinates: [141503 - 155087)
Writing chloro 
```



## 20.3 MBG  -k 4001 -w 250 -a 5 -u 150 


![](https://i.imgur.com/vpCj09T.png)


## 20.4 MBG  -k 5001 -w 250 -a 5 -u 150


![](https://i.imgur.com/1LGM64K.png)


## 21. lpOreTrif1 MBG  -k 5001 -w 250 -a 5 -u 150

```
(biopython) mu2@tol-head2:/lustre/scratch124/tol/projects/darwin/data/monocots/Oreojuncus_trifidus/working/lpOreTrif1.hicanu.20220209/mbg.allreads$ python /software/team311/mu2/join_segments.py lpOreTrif1.trimmedReads.fasta.gz.5k.fa  chloro lpOreTrif1.trimmedReads.fasta.gz.5k.gfa  chloro.fa
Collecting sequences from lpOreTrif1.trimmedReads.fasta.gz.5k.fa
Reading links from lpOreTrif1.trimmedReads.fasta.gz.5k.gfa
=======================================
Processing  20+,19-,18-,19+
20+ 19-
================== Basic step
20+ 19- 7215M
From cigar 7215
Added coordinates: [105639 - 136219)
19- 18-
================== Basic step
19- 18- 7350M
From cigar 7350
Added coordinates: [136219 - 151992)
18- 19+
================== Basic step
18- 19+ 7350M
From cigar 7350
Added coordinates: [151992 - 182437)
Writing chloro
```

```
mu2@tol-head2:/lustre/scratch124/tol/projects/darwin/data/monocots/Oreojuncus_trifidus/working/lpOreTrif1.hicanu.20220209/mbg.allreads/MitoHifi-chloro$ echo ' singularity exec --bind /lustre/:/lustre/ /software/team311/kk16/images/mitohifi-v2.2.sif mitohifi.py -c chloro.fa -f NC_061347.1.fasta -g NC_061347.1.gb -o 11 -t 12 -a plant' | bsub -n12 -q normal -R"span[hosts=1] select[mem>55000] rusage[mem=55000]" -M55000 -P team311 -o mito.%J -e er.mito.%J
Job <601447> is submitted to queue <normal>.
```

![](https://i.imgur.com/uXPBvry.png)


# 22. Chloroplasts

## 22.1 Juncus effusus
```
# Related mitogenome is 170612 bp long and has 130 genes
contig_id       frameshifts_found       genbank_file    length(bp)      number_of_genes was_circular
final_mitogenome        atpF;rps16;rpl20        final_mitogenome.gb     148921  101     False
```
![](https://i.imgur.com/8uI0J2R.png)


## 22.2  Ballota_nigra

```
# Related mitogenome is 151829 bp long and has 132 genes
contig_id       frameshifts_found       genbank_file    length(bp)      number_of_genes was_circular
final_mitogenome        rps16;atpF      final_mitogenome.gb     140570  108     False
```



MitoHifi


```
gfatk_linear    mitofinder      gene    25923   26981   .       -       0       Name=psbA gene 
gfatk_linear    mitofinder      CDS     25923   26981   .       -       0       Name=psbA CDS 
```

Hmm domains
```
gfatk_linear:path=2-,1+,2+,3+:coverage=5634     fppa    CDS     26981   25926   1072.5  -       0       Name=psbA
gfatk_linear:path=2-,1+,2+,3+:coverage=5634     fppa    CDS     58675   59177   69.1    +       0       Name=psbA
```


# 23 Submitting

## 23.1. drMedArab1

Mito from Yaqi's work: 

```
/lustre/scratch123/tol/teams/tola/users/mu2/organelles-submit/drMedArab1
```

```
'drMedArab1_k=1001a=5w=250u=150_extract_mito.assembled.fa'
```
## 23.1. daLycEuro1


## 23.2.daScuGale1
![](https://i.imgur.com/rp1emS6.png)



