# 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)