NOVOPlasty INVALID SEED, PLEASE TRY AGAIN WITH A NEW ONE

INVALID SEED, PLEASE TRY AGAIN WITH A NEW ONE

Open karl1926 opened this issue 2 years ago • 13 comments

Hi, I am getting the error "INVALID SEED, PLEASE TRY AGAIN WITH A NEW ONE". Could you advise?

This is my log:

Input parameters from the configuration file: *** Verify if everything is correct ***

Project:

Project name = 11LV_kmer25_coi Type = mito Genome range = 12000-22000 K-mer = 25 Max memory = Extended log = 1 Save assembled reads = no Seed Input = 11LV_coi.txt Extend seed directly = no Reference sequence = Chloroplast sequence =

Dataset 1:

Read Length = 149 Insert size = 400 Platform = illumina Single/Paired = PE Combined reads = Forward reads = 11LV_R1_merged.fastq.gz Reverse reads = 11LV_R2_merged.fastq.gz

Heteroplasmy:

Heteroplasmy = HP exclude list = PCR-free =

Optional:

Insert size auto = yes Use Quality Scores = yes

Reading Input......OK

Building Hash Table......OK

Subsampled fraction: 100.00 % Forward reads without pair: 273 Reverse reads without pair: 98

Retrieve Seed...BUILD2

INVALID SEED, PLEASE TRY AGAIN WITH A NEW ONE

And this is my seed (the COI sequence for the very same organism that I already sequenced):

1122_ML29D TCAACAAAATCATAAAGATATTGGAACATTATATTTTATCTTCGGTATTT GAGCAGGGTTAGTTGGTACTTCATTAAGATTAATAATTCGAACAGAACTA GGTAAACCCGGTTCACTGTTAAATGATGATCAACTATACAATGTAGTAGT AACTGCTCACGGGTTTATTATAATTTTTTTTATGGTTATACCTATTATAA TTGGGGGATTCGGAAACTGATTAGTGCCTATAATACTAGGTGCCCCAGAT ATAGCTTTCCCACGTATAAATAATATAAGATTTTGATTGCTTCCCCCTTC ACTGACACTTTTATTAGCTTCATCTGCTGTAGAAAGAGGAGCTGGTACAG GATGAACAGTGTACCCCCCATTATCTAGAAATCTTTCTCACGCAGGACCG TCTGTAGATTTAGCCATTTTTTCACTTCATTTAGCTGGTATTTCTTCAAT TTTAGGAGCAATTAATTTTATTACAACTATTATAAATATACGATGAGAAG GTTTATTAATGGAACGAATATCTTTATTCGTCTGATCTGTGTTCATTACA GCAATTCTATTATTACTATCTCTTCCTGTTTTAGCTGGAGCAATTACAAT ACTTCTTACTGACCGAAACTTTAATACTACTTTTTTTGACCCTAGAGGAG AGAGATCCAATTTTATATCAACACCTATTCTGATTTTTTGGTCACCT

Aug 04 '21 17:08 karl1926

Hi, Nothing wrong with the seed.

Or there are no mitochondrial reads or maybe read ids are not recognised.

Could you send a few reads from the forward and reverse files? And you are using the latest version?

Aug 10 '21 15:08 ndierckx

Hi Nicolas, I mapped my reads with bwa on a related species mitogenome and I have mapped reads. I also mapped against the very same COI and used a mapped read as seed and I had the same error.

This are my fastq file heads:

R1:

@NDX550293_RUO:84:HCCHVBGXJ:1:11101:23176:1036 1:N:0:TGGTACCTAA+AGTACTCATG ANTTAGTCCTGCTCAGCAAGGTTTTTGCCCCTAAAATTGAGAGAATTTTTCCAAACCAAAGCGTTCTTGCANCCAACTTNAAGCTCTTGATNTGAGGAATTCACAAATTCAAAATTTATTCAAATTCAGAGAAACGCGTCTGTCTCTTA + A#AAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE#EEEEEEE#EEEEEEEEEEE#EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEE/ @NDX550293_RUO:84:HCCHVBGXJ:1:11101:17521:1042 1:N:0:TGGTACCTAA+AGTACTCATG GNATTATTTGTAATGTCACGCATATCCATACACTAAACTAGGTGTTTTAATTGATAATAAATTAGCCTTTTNACCCATTNAAAATATGCCTTTTTCATCAATTTTTAACATTTGAAGCTGTCTCTTATACACATCTCCGAGCCCACGAG + A#AAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE#EEEEEEE#EEEEEEEEE6EEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEAEA @NDX550293_RUO:84:HCCHVBGXJ:1:11101:15151:1042 1:N:0:TGGTACCTAA+AGTACTCATG CCGGTCCCTTCCCCTTCAGTTTCATCTTTTGACCCTGCCAACTTCAGTTTCATCTTTTGACCCTGCCAACTNCTGCTGANAACCCTAGGAATGGCTGAAATATACTGAAACCTACATTGATATGTGGCGAAGGCTATTCGCCATTTATG + AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEE#AEEEEEE#EEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEAEEEEAE<AEEEEEAA @NDX550293_RUO:84:HCCHVBGXJ:1:11101:15198:1043 1:N:0:TGGTACCTAA+AGTACTCATG ATCTTCATCATGATTAAAAGTTGCTTTTTAGAATTGGAATATAGTCCTACGATAACGATTAAACAGCGTCANCAGAAAGNGGAGTGAGGTTCAAGGCCTTAATTGGGTTCGGTTCCAACCATGGATTTTCGTAGTCCAGTTAGTTAGAA + AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE#EEEEEEE#EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEAEEEEAEEEEEEEEEAEE @NDX550293_RUO:84:HCCHVBGXJ:1:11101:9912:1045 1:N:0:TGGTACCTAA+AGTACTCATG ACACCACGGTAAGTAAGGAATATCTTTACCCCAAAAGATTGGGGTGAACCATGATGAAACTTGCAGAATATNTCAAACANTCTATCCTAACACATGGGTTTCTAAGGAGTATCTTTACCCAAAAAGATTGGGTTGAAATCATGATGAAA + AAAA///A/EEEEAEE6/EA/EE<EAAEEE///EA/EEEAAEEEEEEE/E/EEE/A///EEEE///EAEE<#//EEE<E#EA//E/<E//A/E6//EEA/E/</AEEEEA//E/<E/E<A//<//E/E<EAA/<<</</<//EEEEE// @NDX550293_RUO:84:HCCHVBGXJ:1:11101:10353:1048 1:N:0:TGGTACCTAA+AGTACTCATG AAATAATACTGTGGGAAAGAAAGAAGCATGAGATTTGAAAAAATAATTTTGGTCAAAAATCTGGAGATTTANTGCCTTCNAATGATAAAAATTGACGAAAAAGGCATATTTTGAATGGGGGAAACGGCTAATTTATTATCAATTAAAAC +

R2:

Aug 11 '21 09:08 karl1926

Hi,

The problem is the read id Both paired files have the pattern of the forward ID: 1:N:0 instead of 1:N:0 and 2:N:0 This could confuse other tools too, because this must be a mistake. I would recommend to change the R2 file to 2:N:0 You can do this with a simple bash command or little python/perl script

Aug 13 '21 13:08 ndierckx

Hi Nicolas, I edited my R2 fastq.gz files in bash with the command: zcat $file | sed 's/1:N/2:N/g' | gzip > output/${file}

Now my fastq files looks like this:

R1:

@NDX550293_RUO:72:HCGVHBGXJ:1:11101:16368:1142 1:N:0:5 ACATAGTTTTCTACTTTGGAAATGTTTACCATGTGGAATCAAGCTGAATAATTGAGAAATTGAAAATGATCAAATTCTGAATAGCAATATTTTGGCACGTATTAGCTACTCCTGGCTTGATATTGTATAAATACATCCATTTTGTTCAT + AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<AEAEAEAAEEEEEEEEEEEEEEEEEEAAEEEAAAA<<A @NDX550293_RUO:72:HCGVHBGXJ:1:11101:19351:1156 1:N:0:5 CATTAAAAACTCCAGATTTTTGACCAAAATTATTTTTTCAAATCTCATGCTTCTTTCTTTCCCACAGTATTATTTGTAATGTCACATATATACATACACTAAACTAGGTGTTTTAATTGATAATAAATTAGCCTTTTGACC + AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEE<AAA<AEEEEAAA @NDX550293_RUO:72:HCGVHBGXJ:1:11101:11740:1228 1:N:0:5 CATAGTTTTTGTTTTATTCATTTTAAGACCTACCTTCTTACTTTCTCTATTTAGATCAGCTAGCATTTGCTGTAGTTCTGCTGGAGTTTCAGTAGTAGTGGATATGTCATCGGCGAATCTCAGAAGGTTTAAATGTTCTCCGTCTATGT + AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEAAEEEEEEAEEA<AEEEAEAEAAEEEEEEEEEAEEEEEAEAA<A<EEEEE

R2:

@NDX550293_RUO:72:HCGVHBGXJ:1:11101:16368:1142 2:N:0:5 GCAGATCTTCCGACTCCACTACTCAAGTAACCATTGCCAGCTAACCCTGGACTGACTCTTTTTAAATCTTGGGTCAAATCTTGGGTTTTTAAAATCTTGGTTGAATAAAAGTATAGTNTTATATGCTTATCCATGAACAAAATGGATGT + AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAE6AEEEEEEEE<#<A<AEEEAEAAAEAAAEEEEEEEEEEEEAEE @NDX550293_RUO:72:HCGVHBGXJ:1:11101:19351:1156 2:N:0:5 GGTCAAAAGGCTAATTTATTATCAATTAAAACACCTAGTTTAGTGTATGTATATATGTGACATTACAAATAATACTGTGGGAAAGAAAGAAGCATGAGATTTGAAAAAATAATTTTGGTCAAAAATCTGGAGTTTTTAATG + AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAE<EEEEEEEEEEEEEEAEEEEEEEEEEEEEEAEEEA<EAEEAEEEEEEEEEEEAEEEEEAEEAEEEEEEE<EA<EEEEAEEEEEAEEEEE @NDX550293_RUO:72:HCGVHBGXJ:1:11101:11740:1228 2:N:0:5 GGAGACACTATATCTCCAAAACTATTCACAGCAAGCCTAGAAAGTACATTCCGAAAGACAGATTGGATGGGAAAAGGGATAAACATAGACGGAGAACATTTAAACCTTCTGAGATTCGCCGATGACATATCCACTACTACTGAAACTC + AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEAEE/EEEEEEAEE<EAAAAE/EEA/AEAEEAEEEEEEAEEAE/EAEEE

NOVOPlasty: The Organelle Assembler Version 4.3.1 Author: Nicolas Dierckxsens, (c) 2015-2020

Input parameters from the configuration file: *** Verify if everything is correct ***

Project:

Project name = 10IC_kmer23_mappedread Type = mito Genome range = 12000-22000 K-mer = 23 Max memory = Extended log = 1 Save assembled reads = yes Seed Input = 10IC_COI.txt Extend seed directly = no Reference sequence = Variance detection = Chloroplast sequence =

Dataset 1:

Read Length = 149 Insert size = 400 Platform = illumina Single/Paired = PE Combined reads = Forward reads = 10IC_R1_merged.fastq Reverse reads = 10IC_R2_merged.fastq Store Hash =

Heteroplasmy:

Heteroplasmy = HP exclude list = PCR-free =

Optional:

Insert size auto = yes Use Quality Scores = Output path = 10IC_kmer23

Reading Input......OK

Building Hash Table......OK

Subsampled fraction: 14.54 % Forward reads without pair: 455 Reverse reads without pair: 222

Retrieve Seed...BUILD2

INVALID SEED, PLEASE TRY AGAIN WITH A NEW ONE

Aug 16 '21 19:08 karl1926

Hi, Sorry forgot to reply to your last message. Must still be a problem with read ids, as you can see only 14% of the reads were used. If you weren't able to assemble it yet, you can always send me the data and I can have a look at it

Sep 20 '21 11:09 ndierckx

Hi, I have the same error of invalid seed. Did you figure out the source of the problem?

My mitochondrial read ids do not seem to be confusing. You can see below "1:N:0" for R1 reads and "2:N:0" for R2 reads:

R1 reads

@A01045:607:HK55MDSX2:1:2678:3134:37012 1:N:0:GCTTGATCGA+TGGCACTAAG TGGTCAGAGTTAACCAAGACAAAATAATTACTCCATGAGTTCCTGAAAAGCAGGCACAGACAGTCTGTTGATCACGTGACATGCTGGCAAGCCGAGACTGTTGTTTACATCCGATCCAATTGCAAGAGTACATGCGCACCAACATATAGT + FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFF @A01045:607:HK55MDSX2:1:2678:12120:37012 1:N:0:GCTTGATCGA+TGGCACTAAG CAACGCTACCTCAGATAACTCCCATAATCCACTTTGGTGTGAACTGGGATTACCGTCACTGGACAAGTCACAATCTACTGTACAATAGTACTGCGTTTCATTTTTGGAAAACAATATAGCGAGCAATAGTGTCCCAAAATAACCCATTTT + FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF,FFFFFFFFFF:FFFFF,FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF::FF @A01045:607:HK55MDSX2:1:2678:25626:37012 1:N:0:GCTTGATCGA+TGGCACTAAG AAAAATTCAGTTTAAGATTCATGCTTTTAAAAATTACTTATTATCTTAAATAAATAAACGAATAGAGAGTGTGTCTGACTATGAGTTTGTGTGTGAGTGTGTGTGTGAATGTGTGTGTACATGTGTCTGTATCCTTTATGGAACCTCATT + FFFFFF,FF,:FFFF:FF,FFF,F,F,FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF::,FFF:F:FFFFFFFFFFFF,FFFF:FFF:,FFFFFF:FFFF:,,FFF,FFFFFFFFFFFFFFF:FF,FFFF:F:F,FFFFF,

R2 reads

@A01045:607:HK55MDSX2:1:2678:12120:37012 2:N:0:GCTTGATCGA+TGGCACTAAG TGGCTTTTTCTCGGAAACTATTATAGATTTTCCTTTGAAATTTGGCATACTGGTAGCCCGCGTGAAACTTCACGGCTTGGTATACGTTTAGTTGACCTTGACTAATATTCAAGGTCACAATATGAGAAAAACTGCTTTTTTTGGGCAAAA + FFFFF:FFFFFFFFFFFF:F:FFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,FFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFF:FF:F:FFFFFF:FFFFF:FF, @A01045:607:HK55MDSX2:1:2678:25626:37012 2:N:0:GCTTGATCGA+TGGCACTAAG GAACTGCGGCTAAATGAGGTTCCATAACGGATACAGACACATGTACACACACATTCACACACACACTCACACACAAACTCATAGTCAGACACACACTCTATTCGTTTATTTATTTAAGATAATAAGTAATTTTTAAAAGCATGAATCTTA + FFF:FFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFF:FFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFF,F:F:FFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFF:FFF @A01045:607:HK55MDSX2:1:2678:30617:37012 2:N:0:GCTTGATCGA+TGGCACTAAG CAGTATGACTAATTGAGATATTATTGTGTTGGTTATTTCATCGAGTCGTAGTAGCAGTATGACTATTTGAGACATTATTGTGTTGTTTATTTAATCGAGTCGTAGTAGCAGTATCCTATGACTATTTGAGACATTATTGTGTTGGTTATT + FFFFFFFFFFFFF:FFFF,FF,FF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFF:FFF:,FF,FF:FF,,:F,FFF:FF,FF::F,FFFFF,FFF:,:,FF:,,:F:F,FFFFFFFF,:FFFFF:FFFFFFF,F:FF

I get the error message "invalid seed" when I use COI as the seed. To the contrary, I don't get the error message when I use a full mitogenome as the seed (log_4.txt). The assembly works, but it is poor (2 contigs, 2966 bp in total when they are merged).

I tried 3 different COI seeds:

COI (1000 bp) from another genus than the species being assembled (log_1.txt)
COI (1539 bp) from another genus than the species being assembled (different genus than in 1) (log_2.txt)
COI (620 bp) from the same genus, another species (I don't have sequence data from the species I am assembling) (log_3.txt)

I get the error message for the three seeds.

To be noted that seed 1, as well as the reference mitogenome, have previously worked for assembling another species. The reads for the previous assembly came from another batch of sequencing, and the fastq files were 3.03 Gb each. In the present assembly, the fastq files are only 1.53 Gb each. Could the amount and/or quality of raw data be the cause of the problem of invalid seed?

Seed 1

lit_sax_co1 ATGCGTTGGTTATTTTCAACAAATCATAAAGATATTGGAACATTATATATTTTATTTGGT ATATGATCTGGGCTTGTTGGTACTGCCTTAAGCCTTCTTATTCGAGCTGAACTGGGCCAG CCTGGTGCTCTCCTAGGAGACGACCAGCTGTACAACGTTATTGTTACAGCTCATGCTTTT GTAATAATTTTTTTCCTAGTTATACCTATGATAATTGGTGGATTCGGAAATTGACTTGTA CCTTTAATATTAGGAGCACCCGATATAGCATTCCCACGTTTAAATAATATAAGCTTTTGA CTCCTCCCCCCTGCTTTGCTACTGTTATTGTCTTCGGCAGCGGTAGAAAGTGGCGTAGGA ACAGGCTGAACTGTATACCCCCCTTTGTCCGGAAATTTAGCTCATGCTGGAGGCTCTGTA GATCTGGCTATTTTTTCTCTCCATTTAGCTGGTGTTTCATCTATTTTAGGAGCTGTAAAC TTTATTACAACTATTATTAATATACGATGACGAGGTATACAATTTGAACGATTGCCTCTT TTTGTTTGGTCAGTAAAAATTACAGCCATTCTTCTACTTCTATCCCTTCCTGTTTTAGCA GGGGCTATTACAATATTACTAACCGATCGAAATTTTAATACTGCTTTCTTCGATCCTGCT GGGGGAGGAGACCCTATTCTCTATCAACACTTATTTTGATTCTTTGGCCACCCAGAAGTA TATATTTTAATTCTCCCTGGGTTTGGTATGATTTCCCATATTGTTAGTCATTACTCTGCT AAAAAAGAAACTTTTGGAACTTTAGGTATAATTTATGCAATACTTGCTATTGGTGTTTTA GGCTTTATTGTATGAGCCCACCATATATTTACAGTAGGTATAGATGTAGACACACGAGCT TATTTTACTGCAGCTACAATAATTATTGCTGTCCCAACAGGAATTAAGATTTTTAGTTGA TTAGCCACAATCCATGGAGCTAAAATCAAGTACGAAACTC

Seed 2

lae_ant_co1 ATGCGTTGATTATTTTCGACAAATCACAAAGATATTGGAACTTTATATATTTTATTTGGTATATGATCAGGTTTAGTTGG TACTGCTTTAAGTTTATTAATTCGTGCTGAATTAGGGCAACCAGGTGCTTTATTGGGTGATGATCAATTATATAATGTAA TTGTTACAGCTCATGCTTTTGTAATAATTTTCTTTTTAGTAATACCTATAATAATTGGGGGATTTGGTAATTGATTAGTG CCGTTAATATTAGGTGCTCCTGATATAGCTTTCCCTCGACTTAATAATATAAGTTTTTGATTACTTCCTCCAGCTTTACT ATTACTTTTATCATCTGCTGCTGTAGAAAGAGGGGTTGGTACAGGTTGGACAGTTTATCCTCCTTTATCAGGAAATTTAG GACACGCAGGAGGTTCTGTTGATTTGGCTATTTTTTCACTTCATTTAGCAGGAGTTTCTTCTATTTTAGGAGCTGTAAAT TTTATTACAACTATTATTAATATACGATGACGTGGTATACAATTTGAACGTTTACCTCTTTTTGTGTGGTCTGTAAAAAT TACAGCTATTTTACTTCTTTTATCTTTACCTGTATTAGCTGGGGCAATTACTATACTTTTAACTGATCGAAACTTTAATA CTTCTTTTTTTGATCCAGCAGGAGGAGGAGATCCCATCCTTTATCAGCATCTTTTTTGATTTTTTGGACACCCTGAAGTT TATATTTTGATTTTACCGGGATTTGGGATAATTTCACATATTGTAAGACATTATTCTGCTAAAAAAGAAACATTTGGTAC TTTAGGAATAATTTATGCAATGTTATCTATTGGTATTTTAGGTTTTATTGTATGAGCACATCATATATTTACTGTAGGTA TAGATGTTGATACTCGAGCTTATTTTACAGCTGCAACTATAATTATTGCTGTACCTACAGGAATTAAAGTATTTAGCTGA CTTGCTACTATTCACGGAGCTAAAATTTCATATGAAGCTCCTATACTGTGAGCTTTAGGATTTATTTTTTTATTTACTGT AGGAGGTTTAACTGGAATTGTATTATCAAATTCTTCATTAGATATTATATTACATGATACTTACTATGTAGTAGCTCATT TTCATTATGTTCTTTCTATAGGGGCCGTTTTTGCTTTATTTAGAGCATTTACTTACTGATTTCCTTTATTAAGGGGAGTA AGATTACATTCTCGATGAACAAAAGCACATTTTTATGTTATATTTATTGGTGTAAATGTAACTTTTTTTCCTCAACATTT TTTAGGTTTAAGAGGAATACCTCGTCGTTATTCAGACTATCCTGATTGTTATACTAAATGAAATGTAGTTTCTTCAATTG GGTCTATAATTTCTTTTATTGCTGTTTTATACTTTATAGTTATTGTTTGAGAAGCTTTAATTTCTCAACGAAGAGTAGTT TGAAGAACACACTTAAGTACTGCTTTGGAATGAGATAACATTCTTCCTTCTGATTTTCATAATGCCCCTGAAACTGGAGC TTTAGTTGGTAGTTATTAA

Seed 3

lae_cal_co1 TTTGGTATATGATCTGGTTTAGTGGGGACAGCTTTGAGTTTATTAATTCGAGCAGAACTAGGACAGCCTG GGGCTTTATTAGGGGATGATCAGCTATATAATGTAATTGTAACAGCCCATGCTTTTGTAATAATTTTCTT CTTAGTTATACCTATAATAATTGGAGGATTCGGAAATTGGCTAGTTCCCTTAATGTTAGGGGCTCCGGAT ATAGCTTTTCCTCGCTTAAATAATATAAGTTTCTGATTATTACCTCCTGCGCTCCTTTTACTTTTATCTT CTGCAGCTGTTGAGAGAGGGGTTGGAACAGGGTGAACTGTATATCCTCCTTTAGCTGGAAATTTAGCTCA TGCTGGAGGTTCTGTAGATTTAGCAATTTTTTCTCTCCATTTAGCTGGTGTTTCTTCTATTCTAGGAGCA GTAAATTTTATTACTACAATTATTAATATGCGTTGACGGGGAATGCAGTTTGAGCGTCTTCCTTTATTTG TATGATCTGTTAAAATTACTGCTATTTTGCTTTTACTTTCTCTTCCGGTTTTAGCTGGTGCGATTACAAT ACTTCTTACTGATCGTAACTTCAATACTTCTTTTTTTGACCCGGCAGGAGGAGGAGACCC

Reference

lae_ant_ref mitochondrion, partial genome ATGCGTTGATTATTTTCGACAAATCACAAAGATATTGGAACTTTATATATTTTATTTGGTATATGATCAGGTTTAGTTGG TACTGCTTTAAGTTTATTAATTCGTGCTGAATTAGGGCAACCAGGTGCTTTATTGGGTGATGATCAATTATATAATGTAA TTGTTACAGCTCATGCTTTTGTAATAATTTTCTTTTTAGTAATACCTATAATAATTGGGGGATTTGGTAATTGATTAGTG CCGTTAATATTAGGTGCTCCTGATATAGCTTTCCCTCGACTTAATAATATAAGTTTTTGATTACTTCCTCCAGCTTTACT ATTACTTTTATCATCTGCTGCTGTAGAAAGAGGGGTTGGTACAGGTTGGACAGTTTATCCTCCTTTATCAGGAAATTTAG GACACGCAGGAGGTTCTGTTGATTTGGCTATTTTTTCACTTCATTTAGCAGGAGTTTCTTCTATTTTAGGAGCTGTAAAT TTTATTACAACTATTATTAATATACGATGACGTGGTATACAATTTGAACGTTTACCTCTTTTTGTGTGGTCTGTAAAAAT TACAGCTATTTTACTTCTTTTATCTTTACCTGTATTAGCTGGGGCAATTACTATACTTTTAACTGATCGAAACTTTAATA CTTCTTTTTTTGATCCAGCAGGAGGAGGAGATCCCATCCTTTATCAGCATCTTTTTTGATTTTTTGGACACCCTGAAGTT TATATTTTGATTTTACCGGGATTTGGGATAATTTCACATATTGTAAGACATTATTCTGCTAAAAAAGAAACATTTGGTAC TTTAGGAATAATTTATGCAATGTTATCTATTGGTATTTTAGGTTTTATTGTATGAGCACATCATATATTTACTGTAGGTA TAGATGTTGATACTCGAGCTTATTTTACAGCTGCAACTATAATTATTGCTGTACCTACAGGAATTAAAGTATTTAGCTGA CTTGCTACTATTCACGGAGCTAAAATTTCATATGAAGCTCCTATACTGTGAGCTTTAGGATTTATTTTTTTATTTACTGT AGGAGGTTTAACTGGAATTGTATTATCAAATTCTTCATTAGATATTATATTACATGATACTTACTATGTAGTAGCTCATT TTCATTATGTTCTTTCTATAGGGGCCGTTTTTGCTTTATTTAGAGCATTTACTTACTGATTTCCTTTATTAAGGGGAGTA AGATTACATTCTCGATGAACAAAAGCACATTTTTATGTTATATTTATTGGTGTAAATGTAACTTTTTTTCCTCAACATTT TTTAGGTTTAAGAGGAATACCTCGTCGTTATTCAGACTATCCTGATTGTTATACTAAATGAAATGTAGTTTCTTCAATTG GGTCTATAATTTCTTTTATTGCTGTTTTATACTTTATAGTTATTGTTTGAGAAGCTTTAATTTCTCAACGAAGAGTAGTT TGAAGAACACACTTAAGTACTGCTTTGGAATGAGATAACATTCTTCCTTCTGATTTTCATAATGCCCCTGAAACTGGAGC TTTAGTTGGTAGTTATTAATGATATGAGTCTATGAGGACAATGAGGATTTCAAGATGCAGCTTCTCCTTTAATAGAGGAA TTAATTTTTTTTCATGATCATGCAATAATAATTTTAATTATAATTATTAGATTAGTAGGATATGCGGCAGTTTCTTTAGC TATAAATAAGTATACTTGTCGTTCATTAGTGGAGGGTCAAGAAATTGAAACAATTTGAACTATTGTTCCTGCTTTTATTT TAATTTTTTTAGCACTTCCATCTCTTCGTCTTCTTTATTTATTAGATGAAGTTGGAGATTGTGGATTAACTATTAAAAGT ATTGGTCATCAATGATACTGAAGTTATGAATATTCAGATTTTTTAAATATTGAATTTGATTCTTATATAATTCCTACTAC AGACTTATCTAGTGGTGATTTTCGTTTATTAGAAGCCGATCATCGGGTTGTTCTTCCGACAGAAACAGATATTCGAGTTC TTGTAACTTCTGCTGATGTAATTCATTCCTGAACTGTACCTTCACTTGGTGTTAAAGCAGATGCGGTTCCAGGTCGATTA AATCAATTAAGATTTTATGTTAAATACCCAGGTATTTTTTATGGACAATGTTCAGAAATTTGTGGGGCTAATCATTCTTT TATGCCGATTGTAGTTGAAGCCGTACCTTTAGAAAATTTTATAAAATGGGTAGTTCAAGTATCTGAATAATTTAAAGAAG TTAGTTAAAATATAATATAAGATTGTCAGTCTTTAGTTACTAGAATACTAGTATTTCTTATATGCCTCAATTATCCCCAC TTAATTGAATTTTTCTATTTATTTTATTTTGAACTGCGGTAATTATAATTTCTATAATTATTTGATGATCTAAAAAAACT TATTTCTTAGCTGAATTGTCTCCTGTTAAAGAAATAAAAGAAAATAAGTGAAATTGATAAGAATGCTAGTTGACATTTTT TCTTCATTTGATGATAACAACCAAGTTTTTATATCTTTATATGCTTTAATGTGAGTATTTTCATTAAGTATAATTTTTAT TTTTAGTTCTAGCTATTGAGTAGTTAATCCTGGTTGAAATTCTGTAATTTATTTATTTAAGGATACAGCAACATCTCAAG TTTTTCGGTCTTTTGGTTTAAAGTTAGGAGGATTTTTAAATTTAATTACAGCTTTATTTTTATTTCTTATTTTTATAAAT TTAAGGGGGTTGGTTCCTTATGTTTTTAGTCCAACAAGTCATTTAGCAGTTTCGCTTGCACTAGGTCTTCCCTTATGACT TAGTTTAATTATTTCTGCAATTTTTCTTAACCCTAGTTCAGTTATTGCAGGATTATTACCTATAGGAGCTCCTGCTCCTT TAAATCCTTTTTTAGTTGTTATTGAGACAGTTAGAATTTTAGTACGTCCTATTACACTATCTGTACGACTTACTGCAAAT ATAAGAGCAGGACATATTGTCCTTACTCTTATTGGTAATTATTTAACTGCAAGTTTTTTCTTACCCGGTATTATGTCTAT AGCATTTTTACTTATAATTCAAATTTTTTATACTATTTTTGAATTCGGTATTGGTATTATTCAAGCATATATTTTTTGTT TACTTATCACATTATATTCTGATGAGCATCCTATATAAATGTATAAATATAACTTTTTTTAAATGTTATTGTAAAAGAAC TTTGTTCATTTTTGAGGTATGAGCCCAATAGCTTTACTTAGCTTATTTTACATTTTGTTGAGAAAATTTAATTTCGTAAT TAGATCTACAGTCTAGTGCCTATATTCTCAGCCATCAAACAAGATCTATTGGGATTACTTAGTCCTTCTCCGAGCTTGCA ACTCAGAATTTTAATTATAAAATACAACAGTTCAAGATTTGAAAATTTTATTTCATATTAAGCTTTGAAGGCTTATAGTT TATTTAACTTAAAATCTTACTAGGAGGAAATGACCCTCTCTTAAGAAATCAAAATTCTTTGTGCCCTCACACCGCTTGTA ATATCTCTTTTAAATAGATTTAATCTTTTTGCTTGGAAGGCAAATGTACTTATAATACTTAAGAGATATTTCTAATAAAA ATATTTTATTCTTTTAAACTGAAAATTTAATGTGCTGTGTGACACCATAGAAACTTTAATTAACTAATATGTGCTTTAAA TATATCAAGTATATATATTAAATTCACAATTATATTTATCTATAGTATAGCTTGGCTCTGACTTAAAAGCATATCGAAGA CAAAGAAACACACATGGTTTTTATTGAAAGGGGTGAGAAAAAAGATTTAATATTTTTAGTTTATAACTAATTATAGTGAA ATTTTTTAAGGTTATAGTATATACAATCTTTAAGGTAACTCACTAACACCAGTGTCAGATTTTAATTATGAGCGAAAGTT TGATTTAGATTAGTTTTTCAGGTTTGGTTAATTTGGTGCCAGCATCCGCGGTTAGACCAATAAATCAAGTTATGCTTTAT AGGTAAAAAGATAGTTAAATATTTATAAGTTTTAAAATTTCTTATTCCTAAGTAAAATTTGTAAATAAGAGAAATTTCTT AATAAAACTACTATATTGAAGCTATGAAGGCTTAGAGGGAAACTAGGATTAGATACCCTATTATTCTTTGTTACAAATTA ATAAATATTTACCAGAGTACTACAAATAAAGTAATTTAAAACTCAAAGAGCTTGGCGGTGCCTTAGACCTCTCAGGGGAA CTTGTCCCGTAATCGACAACCCACGTTAGACCTCACCTTTTTTAGCAACTCAGTTTGTATACCGTCGTCGTCAGGTAACT TTTAAAAATATAAAAGTTAGCATTATAAAGTTTTAGCTTTATACGTCAGATCAAGGTGCAGCTTATAAAAAGAGGCGTGG ATGAGTTACAATTAAAATTCATAATACGAATAATATTTTTAAATAAATATATTGAAGGAGGACTTGAAAGTAAAGATAAA TATACAAATTTCTTGAATCTGGCTCTAGGGCGTGCACACATCGCCCGTCGCTCTCGTTGAAAAATGAGATAAGTCGTAAC ACAGTAGGGGTAATGGAAATTGTCCCTAGGTGAAAGAAAATAGCATAAATTAATGTATTTCATTTACACTGAAATGATGC TTATTAAAAGCTTTTCTTATATAAATTTAAATAGTTATAAATATATGTTATTTAGATATGAAACATCTTTTAATAGTGTA CTGGAGAAAGACATTTTATAAATAAAACTATTTAAGTACCGCAAGGGAATTAAATTTAATTACATTTAAATAATAATCTT AATATGTACCTTTTGTATCATGGTTTAGCTAGATATTTTTTAGAAAAAATTTCTCGAAATCTAATGAGCTACTTTTTTTA GTATATTAGTGCACAAAAATAACTGTGGCAAAAGTTTTTCTATAAAAAAAGGTAGCAATGAAATTTTATTCGTATTAGAT GATAGCTAGTTTTCTTTAAAATACATAGAAGTGTGAAGGTCTTTTAAATTACATATAAAATTTTATATATAATATAAAGA ATCTGCAGATTTTTGAGGATAAGCTCGAAAATAAATTTAAATCTTGCATTAATTATAACATTAAAATCTAAGCTTGAAAC TAGCTAATATTGAAATTATGTTACAATTTATTAATGGTTAAATAAAAATTAATATGCTTAAACTTAAAAGAAACTAATTA TAAACTTAATTAATTAAGAATAATGCTAAAATGAGTATTATTAATATATGAAATTTAGTTTATTAAAAACTAAAATTTAT AATAAAATTTTTTTATTAATTTTTATGAAGGAACTCGGCAAATAATTTGCTCTGCCTGTTTATCAAAAACATCGCTCTCT GATTATATAATATAGAGAGTCGGACCTGCCCAGTGATATAAATTTAACGGCCGCGGTACTCTGACCGTGCAAAGGTAGCA TAATCATTTGCCCTATAATTGAGGGCTAGTATGAAGGGTTTGACAAGAGCAAAACTGTCTCCGTAAAAATTTATATAAAT TATTTTTTAGGTGAAGAAACCTAAATTTTATTAAAAGACAAGAAGACCCTATCGAGCTTTAAATTTATTTTTGTAATAAA AAAATATTTATATATTTCTATACTTAAAAAATTTTGGTTGGGGCGACTAAGGAACAATTAAAGCTTCTTTATATATAAAA CTTATTAGTAGTGACCCGCTACTTTAGCGGTTAAAAGAATTAGTTACCGTAGGGATAACAGCATAATCTTTTTTGAGAGC TCTTATCGAAAAATAGGTTTGTGACCTCGATGTTGGACTAGAATATCCTGACAGATGCAGCAGTCTTCAAGGGTTGGTCT GTTCGACCATTAAAATTCTACATGATCTGAGTTCAGACCGGCGTGAGCCAGGTCAGTTTCTATCTTTAATTTATTTTTAA GCTTAGTACGAAAGGACCAGCTTAAAGCAATTTTTGTTCAACAAGATTTAATATAATAATTATGTTAATATATAAAATAG TGGCAGATAAGTGCATTAGATTTAAGCTCTAAATATAAAGATGAAAATTCTTTCTTTTTTAAATAAAAGTGGCAGATAAG TGCATTAGGTTTAGAACCTAATTATAAAGATTTTATTTCTTTCTTTTATTCATGCTTTTATCATTCATTTCTTCTTTATT TACTTATATCTGTGTATTACTAGCAGTCGCTTTTTTTACTCTTTTAGAACGTAAAGGTTTAAGTTATATACAGATTCGAA AAGGACCTAATAAAGTAGGTATTGCTGGTTTACCTCAACCTTTAGCAGATGCAGCTAAATTACTCACTAAAGAAATTGTA AAACCCACTATAGCAAATTATTTTCCTTATTTTAGAGCTCCTATCTTTAGTTTTATCCTAGCTTTACTTCTTTGGCAACT TTATCCTGGAATATATTCTCTTAGATATTTTAAATGATCTATCTTATTTTTTTTATGTGTATCAGGTTTAAATGTATACG GAACACTTCTTGCAGGGTGAGCTTCTAATTCTAAATATGCTTTATTAGGAAGATTACGTGCTATTGCTCAAACTATTTCT TATGAAGTTAGTATAGCTTTAGTACTCTTATTTCCTTTATTTATTGTTGGAAGATTTAGCTTTATTGAAGTAAAAGAAAT TCAAGTTTTAATTTGATTAATATTTGTAATAATTCCTGTAGCTTTAATTTGATTTGTAACTTGTGTAGCAGAAACAAATC GTGCTCCCTTTGATTTTGCTGAAGGAGAATCTGAACTAGTATCGGGTTTTAATATCGAGTATGGGTCTGCTGGATTTGCA TTAATTTTTTTAGCAGAATATGCTAATATTCTTCTTATAAGTCTGTTAACTTCAATTTTATTTGTGGGAGGTAGTTTTAT ATTATTTATAGAAAGAGATATTATATTTATGCTAAAAATTTTATTTTTTGCTTTTTTATTTATTTGAGTTCGAGGTAGAT ATCCCCGTTTTCGCTATGATTTATTAATAAGTTTAACTTGAAAAAGATTTTTACCTGTAGCATTAAGTATACTTTTAATA ATTTTTGCTGTATGTTATATATTTTTATATTAACGAGATTGTAGTTTATAAAAACATCAGCATTGGAAGCTGAAGATTAG AACTTATTCTATGTCTCGAGAATGATACCTAGAATTATTTTGGCTTTTAGATTATCTAGACTTATAATAATTCCTCTTAT ACTTCAACCCCTAAGATTAGGCTTACTTATCATAATTTCTACTTTATTTATATGTATATTAGTAAGTATATTTTTATCTG CTTGATATGGATATATTTTATTTTTAATTTATGTAGGAGGTTTATTAGTTATATTTACATATGTAGCTGCTTTAGTCCCT AATATTTTATTTAAAAGTCTTTTACCCTTAGCTCTTTGTTTTTTTCTTGCTTTTATTATTACTGGATTTATATATTTTTA TCCGTTTTTGGATACAAACCAAATTAGGTATACATCAATAATTAGTTTAGATAAAAACATAAAAATATTTGGAGGTCAAT TAGTTTCTCCTCACACTTCTTCTCTTCTTATTGCTTTAGGCCTAATTTTACTATTGAATTTAGTTATTGTTGTTAAAATT TGTTATTATCAACAAGGGTCTCTTCGTCCTTTTAAAAGTTAATATTTATGCGTAGACCTATTCGTAAAATTCATCCAATC TTTAAAGTAGTTAATGGAGCTTTAGTAGATTTACCTGCACCAGCAAACTTATCTATTTGATGAAACTTTGGTTCTTTATT AGGACTTTGTTTAATCATTCAAATTTTAACTGGTTTATTTTTATCTATACACTATACAGCAAGTGTTGACTTAGCATTTA ATTCAGTTATTCACATTACTCGTGATGTAAGAAACGGCTGATTACTTCGTGCTATACATGCTAATGGGGGATCTTTATTT TTTATCTGTATTTATTTTCATATCGGACGAGGTATATATTACGGATCTTACCTATATAATCACACATGAAATATTGGAGT TATTTTATTATTTCTAACTATAGGCACAGCATTTTTAGGCTATGTTCTTCCCTGGGGACAAATATCATTTTGAGGTGCAA CTGTTATTACAAACTTACTATCCGCAGTTCCATACTTAGGTAAAATACTAGTTGAATGAGTTTGAGGTGGTTTTGCTGTT GATAATGCTACATTAACTCGTTTTTTTACTTTACATTTCTTATTACCTTTTGCTATTGGAGGTCTAACTTTTTTTCATCT TTTATTCTTACATGAAACAGGATCTAATAATCCTTTAGGTATTAATAGAGACGGGGAAAAGGTGCCTTTTCACTCATACT ATAGATTTAAAGATTTAGTTGGGTTTTTATGTTTATTATTTTTATTATTAAATTTAGTATTATTTAGACCTCAACTTTTA ACTGATCCTGAAAATTTTATTCCTGCAAATTCTTTAGTAACCCCTGTGCATATTCAACCCGAATGGTATTTTCTATTTGC ATATGCCATTTTACGATCTATTCCTAACAAACTAGGAGGAGTTATTGCTTTAGTTGCAGCGGTAGCTATCTTATTTATTT TGCCTCTAACTCATCAAAGCACTTCTCGATCTTTAGCTATTTATCCTTTTAACCAAATTTTATTTTGAAGATTATTAGGT ATTTTTTTAATTCTCACTTGAATTGGGGCTTGCCCTGTAGAAGCACCCTATGAACAAATTGGTCAAGTATTTACAGTAAT CTATTTTTCTTATTTTTTAATTAACCCATTAACACAAAAAATGTGAGATAATATTTTAGATTTTTAAAATAAAGTTATTT CTCGGAGAAAGTTTGTCTTGAAAACAAACTCAAAGTGTTCAACTCACTTAATAACTTAGTAATAAGAGAAATAATCTCAA TCTTTGGCTTACAAGACCAATGCTTTATATAAGCTATTATTACTGAATGATATGAGAACATTTTCTACAGTTTTTATTAG AACTTTTGGCGTTTTTTCAGCCTTAATTGCTTTAGCTTTACAGTATAAGCATTTATTAAGAATTTTATTGAGCTTAGAAG CAGCCACTATAAATCTATTTATTATAATATTTGCTATAGCTAATAATATCTCAGCAAATGGAGAAATATCTTTAATTTTA ATTACCTTAGGAGCTTGTGAAGCAAGATTAGGACTTGCTATTCTTGTATCTATAATTCGAAGCCAAGGTAATGATTACGT TTTTAGATTTTCATCACAAAAATGTTAGGTATTTATCTTATAGTTTTAAGATGTTTCTTACCCATAAAATTATGTTCTTG ATATACTAAAATTTGAATTTTATCTATTAGAAGAGTGATTTCATTAATTCATATTTTTAGACCATCTTTTTCATTTATAC AAATTAATTCTATAGTTATTTCAGATTCTATATCCTCATCATTAATCAGTTTAACTTTATGGATTTCCCTTATAATATTA ATAGCTAGCCAAAATAGAGTTAAAATTAAAAATAATAAACCTGAAATTTTTTCATGAACTATTATTTTTTTAACTATTAT TCTTGTAATATCATTTTCTACATCTAGAATTATATATTTTTATTTTTTATTTGAAAGTTCTTTAATTCCAACTTTAATAC TTATTTTAGGCTGAGGTTACCAACCTGAACGACTACAAGCTGGGATGTATATAATAATTTACACAGTAACTGCATCATTA CCTTTATTATTAGCTATTTTATGAATAATAGAAAAAACTTTTATTTCAAATATTCTTATAGCTTCTACTATTCGAATAGA AAGACTAGTTTTACAGCATTCCTGATCTTTAAACCTTTTTACTTTTATTATTTTTTCTGCTTTTCTAATTAAACTTCCCA TATTTTCAGTCCATCTTTGACTTCCCAAAGCTCACGTAGAAGCTCCAGTTGCCGGATCTATAGTCTTAGCTGCAGTTCTT TTAAAACTTGGAGGTTACGGTATCTTACGAAGATATCAATATTTTAATTTTTATTTTAGAGAATCTTTAATTTTTATATT TTCATTAGCTTTATGAGGAGGCGTTTTAACAAGTATTATTTGTTTTCGTCAAGTTGACTTAAAATCTTTAATTGCATATT CTTCTGTAGGCCATATATCTCTAATAATTGCAGGAGTCTTTTCTAACACTTCTTGGGGATGAGGAGGTGCCTTAGTATTA ATAATTTCTCATGGTTTTTGTTCCTCTGCTTTATTTGCTTTAGCAAACTATACTTATGAAAAAAGACATAGACGAAGATT ATTTTTAACTAAAGGAATTTTAATATTGTTACCTATTTTAGCAATATGATGATTTCTTTTTTCTGTAATTAACATAGCTG CTCCCCCTAGAATCAATTTATTAGGTGAAATTATAATTTTTCCTTCAACTATTTTTAGTTCTACTTACTTTACTCTTTCT CTTGGGCTAATAAGTTTCTTATCAGCTGTTTATAGTATATATTTATATACAGCAAGTCAACATGGAGGAAGTCCTAAATT TATAAAACCTTTTACAAATTTTAATACATCAGGATATTCTTTATTAACATTACATTGATTACCCGCTAATTTTTTAATTT TAAAAAGAGAATTACTATTTTTATGAATTTAAATAAAGTTAGTTTATAAAAAACACCAGCTTGTGGATCTGGAGATAAAA ATTTATTTTACTTTATCATGCTAATAAATCCTAAATCTTCATCTATTAGTTCTTTCATTCTTTTATTTTATAGAATATGC TTATTTCCTATTTCTTGTTATTTTATAATAACAGATTTTTGTTTATTATTAGATTGACAATTAATATTTCTAAGATCTTG TAATATAACTTTTTCTATTATTTTAGATAGGGTAAGATTAAGTTTTAGAAACGTAGTTTGTTTAATCTCAGGATGTGTAT TAATATTTTCATCTAGCTATATAGCTCATGATCCTTTTTTAAAACGATTTATTTTTTTAGTTATACTATTTGTATTATCT ATAAACCTTTTAATTTTTATTCCCAGATTACCAGCCCTTCTTTTAGGATGGGATGGGCTAGGAATTGTATCTTTTGCTTT AGTAATTTACTATCAAAACATAAAATCTTTAAGTGCTGGAATAGTAACAATCTTAGCTAATCGAATTGGGGATGTAATAA TTCTTTTTTCAATTGGTATTCTAGTTTTACAAGGACATTGATTAATTACCTTAATAAATGATTTTTACCTTTCATTTTGA GTAGTTCTTGCTATTACACTAGCCGCTATAACAAAAAGAGCACAAATTCCTTTTTCAAGATGACTTCCTGCTGCTATGGC TGCACCAACTCCTGTATCTGCTTTAGTACACTCCTCTACCTTAGTAACTGCAGGGGTTTTCCTTTTAATTCGATTTTACC CTTTTTTATCCGCTTGTGAATTTTTCAAGCCTTTTTTATTATTTGTATCTGTATTAACCCTTTTAATAGCAGGTATCGGA GCAAACTATGAAAATGATCTTAAAAAAATTATTGCTTTATCTACTTTAAGTCAATTAGGTGTAATAATAATAAGGCTAGG ATTAGGAATACCTTACCTGGCTTTATTTCATCTGTACACGCATGCTCTTTTTAAAGCTTTATTATTTCTCTGTGCCGGAA CTATTATCCATAACAGATCTAATTCTCAAGATATTCGAACTATAGGAATAATTTTTAAACAATTACCTTTTACAATTACT TGTATAAATATTGCAAATTTATCTTTATGTGGTGCTCCTTTTTTAAGAGGCTTTTATTCAAAAGATTTAATTTTAGAACT ATCCCTTTTTCAACCTTGTAATTATATTATAGTAATATTAATTTTTTTAGCAACTGGAATAACCGCAGCTTACTCTTTAC GACTTTCTTTTTGTTCATTATGAGGAGTTACAAAATCTTCTCCTATACATAGCAAATTAGATAAAGATTATTACATTAAT TTCTCGACAGGAATTTTAAGAGTATTAGCAATTGTAGCAGGATTTTTTATACAAAGTTTATTTATTCATTTTGAACCCCC TGTATTTATAATACCAATAAACCTTAAATTATTAACAATTATAGTTATTATTTTAGGAGGATACATTTCAACAGTACTTT GAAATATAGAATTTTCTACTAAACTAGTAACTAAGCTAGACATATTTTTTTCTTCTATATGGTTTTTATCTAGAGTATCA GCACAACCTGTTACTAAAATAGGAATAGTATCTGGTACTAATCTTATAAAATCTGTAGACCAGGGATGGCTTGAAATTCT AGGAGGTCAAGGAACTTATAAAATATTAAGGAAAATATCATTAAATAATCAAAACTTACAAATTATAAATTTTAGTATTT TTATTATAACAATAATTTTTTCTATCTTACTAATTTTATTTTGATATTTTTTTATATATTCAGGTAGTTTAAATTTGAAC GTAGCACTGAAGATGCTAAAGTGGCATTTTTGCCCCAGAATAAAACATTATTTTAACAAAAATTATAGTAAATTAATAAA TATATAAGTAATATAGCTAAATCAACACCACTTATATAAACTTAATTTTACTAGTTTTAAAAAATTCTTTTTTTTTGTAA ACTATACCCTATTTAAAGAAATAGTATACTTATTTTTAAAAATTCGATAAGGTAGTTACCTGCTTAATTTATGTTTTTTG GTGTCACTCGATGTAATTTTTGGCTTTTTGTGCTTAAAAATCTTTTGTAACAAAATTCACTCCAAATTGCTAGATATATC AGTGATATAATTAAATTAGCACTCATTTTTATGAAACTAATTTTTATTAATTTTAGGGGACCCTCTCTCCTCCTAGCGCC ATGTCTTATCTAGAGCAATAAAATACCTAGTTTTTAAGATTTTTATTAATCACCTCTCTGCTTCCACCGGCGTTTTTTTG GGAACGCCGGGCTAACTCGGTATCGAGCTAACCTTAAACACTGTGTACTATGCTTTTTATGACTATATATCACTTTATTT AGATAGGGGAAATAATAGAGCGAAGATATGTAAAAAAAGGGTCAATGACACCAAAAAACGTCGTTTTTTGGTGTCACTCG ATGTAATTTTTGGCTTTTTGTGCTTAAAAATCTTTTGTAACAAAATTCACTCCCCCCTAAAATTAATAAAAATTAGTTTC ATAAAAATGAGTGCTAATTTAATTATATCACTGATATATCTAGTGAATCTAGTAATAATTTTATAATATTAAATAGTGAA ATACTTCATTCAATTATATAATTATATTTCATTTTAGTTTAACTCTATGGCTCGAACACCATTTCATTTAGTTGAGTTTA GTCCTTGGCCTTTAACAGGTTCTATAGGAGCTTTATTTTTAACTTCCGGATTAGCTGGTTGATTTCATAACCATTCTGGG TTGACTGCTATTTTTGGTTTAACTTTAATTATTATAACTATAATTCAATGATGGCGAGATGTTATTCGTGAAGCTACATT TCAAGGTTATCATACTATTCAAGTATCAACAGGTCTTCGGTGGGGTATAATTTTATTTATTGTTTCTGAAATTTGTTTTT TCTTTGCGTTTTTTTGGGCTTATTTTCATAGAAGTTTAGCTCCTAGTTCTGAGCTAGGTTCTTGTTGACCTCCTGCTGGT ATTGTTCCCTTAAATCCTTTTGAGGTTCCTCTTTTAAATACGGGAGTTTTATTAGCTTCAGGTGTAACTGTTACTTGGGC TCATCATAGTATTATGGAAGCAGATCATTCAAGGGGTATTCAAGGGTTAGTAGCTACAGTAATTTTAGGTATATATTTTA CTTTTCTTCAAGGATGTGAGTACTTTGAAGCAAGCTTCACTATTGCTGATGGAGCTTATGGTTCTAGTTTTTTCGTAGCT ACAGGATTTCATGGACTTCATGTATTAATTGGTAGGACTTTTCTGCTTGTATGTTTGGTTCGTATGTATTTTTTACATTT TTCTTCGGGTCATCATTTTGGGTTTGAAGCTGCTGCATGGTATTGACATTTTGTAGATGTTGTTTGATTATTTTTGTACC TTTCTATTTATTGATGGGGATGTTAATAAAATACTTTAGATGACTGAAAATAGGTGCTAGATTTTTAATCTAGTTATGAC AATATTAGAGTTGTCTCTAGAGAAGGTTTAATACTTTAATTTAAAAGATTTGATTTGCATTCAAGAAATAGACTTTTATG TCTTTAAGCCCTGTATAAAAAGCGAGAAATTTGCATTCGATTTCGGCTCGTATCTTAGAGGTGCAAGTCCTTTTTTATAC TTATAAATAAAAGCCAAAACAGAGGCACCTAGCTGTTAATTAGAAGATTGTAAATTATTACTTATTTAGGTGCATTACGC CGGATGAACGGAAATCATTGATGTTGATTAATATAAGGTTATATTACCTTTAATGTTAGATGTCTAGTGTTTTATTTAGA AGCCTTTTTGCTATTTTTTTATCTATTATTGTCATAGGTATTGGTTGAGTCTTAAATAAGCGAAGCTTAAGTGACCGAGA AAAAAGATCCCCTTTTGAGTGTGGATTTGATCCTATTAAGTCTGCTCGATTACCTTTTTCTCTTCGATTTTTTTTACTAG CTATTATTTTTTTAATTTTTGATGTCGAAATTGTTTTATTATTTCCTGTTTTAGTAGGTATAACTTGAGTATATTCTTTA AGTATAATAGTTAGAGCCTTTATTTTTTTATTAATTTTAATTGTAGGGTTATTTCATGAATGAAATGAGGGTTCTTTAGA TTGGGCTCAATAGAAAAAACTTGGAGTAAAATAGGGCTGCTAACTTTATTTTGGGTAATTCAATTTTATCCTTTTTCTTA TGTTTTCAAGTTTACCTTTTGGTTTTATATTTGTATTTACTTTAATCTTTGGTACTTTATTTTCAATTTCTTCTTCTCAT TGATTAGGGGTATGAGCTGGGTTAGAAATTAATTTAATTGGGTTTCTTCCTATGTTAGTATATCAAAAAAGTATGTCTGA AAGAGAATCTGCAGTTAAGTATTTTATTATTCAAGCTTTAGGATCAAGTTTACTTATTTTTGGTAGTCTTATTAGATCCT CACTTAGCTTTGATTGAAGCTATATTGATTTATCTGATTTTTCTGTAATAGGTTATTTTCTTGTTATATTTGGTTTAATT ATTAAAATAGGACTATTTCCTTTTCATTTTTGATTACCTGGGGTTATAGCTGGGTTACCTTGAATTTCATGTATAGTTTT AGCTACTTGACAAAAAGTGGCTCCTGTATTTTTAACTAGATCTTTTTTTGATTTATATTCTATATATTTTTTATTATTAA TTTGTATTTTTTCAAGGGGATCTTCAATTATTGGGGGGTTAGGGGGTTTAAATCAAACTCAAATTCGAGCCATTTTAGCT TATTCATCTATTGGTCATTTAGGGTGAATTATATTTGCACTTAGACAAAGAGATTGAGCCATAAAAACTTATTTTATTAT TTATATTTTAATTTCTTTAACTATTTTTATTTCTTTATGATTTATTGATGTAAAAGAATTAAAAAGATCTAAAAACTTAT CTTCTAATAAACATCATACTATGTCTGTAATACTTATATTACTATCTTTAGGGGGACTTCCGCCTATGCTAGGGTTTGCA TCTAAATGAATTGTAGTATATAGTAGTATAAGTAGAAGTTATTCTTTATTTCTTTGGTTTTTAATTTTGGGTTCTTTAAT TAGTTTATTTTATTACTTAAGTTTATATTTTTCTTTATTTCTATCTTCTTTTAAAGTTACAAGATTTAATAAAGGTTTAA TAATAACTAAAAACATATCAATTAATTTAGGTCTAGTATTTAATTTAATAGGAGGTTTAGTTATTTTACTTAGTAGAATA ACATTAGAAATTTAAATT

Oct 01 '21 17:10 sfourdrilis

Hi,

Sorry didn't had the time to look at it earlier.

What kind of data do you have? is it WGS or is it captured DNA? Because if it is captured, there are often missing regions and then NOVOPlasty won't work well, it needs coverage across the whole mitogenome If it is WGS, it is possible that you just have very low coverage... If you run again with extended log set to 1, I can check that (for the assembly that has two short contigs)

Oct 13 '21 13:10 ndierckx

Hi Nicolas, sorry for getting back to you so late. I am still trying to figure it out what's wrong with my assemblies. It's always worked in the past. I have a doubt: does it work properly with concatenated fastq file? I'll explain better. I have a sequencing A of 700 K PE reads and a sequencing B of 3 M PE reads. They're both from the very same library, just different run. When I concatenate them in order to use it a "larger" fastq file with more reads and info, I always got weird result. If I concantenate in the order A + B, I got a result identifical if running only A. If I concantenate in the order B + A, I got a result identifical if running only B. It seems like there's no improvement given by the larger amount of info. I don't know if I explained myself and the issue properly. Any idea?

Karl

Nov 02 '21 15:11 karl1926

Hi,

That must because the read id structure of both files are different The read id structure gets determended by the first three reads so you should convert one of the two files

Can you send the read id of both files, just first read of each file is ok Maybe I can change something in the code

Nov 02 '21 19:11 ndierckx

Hi, thanks for your prompt reply. That's the identifier:

A_R1:

@NDX550293_RUO:84:HCCHVBGXJ:1:11101:19307:1038 1:N:0:TATGCCTTAC+TAATGTGTCT ANATTACACAGAGACACAAACGAAATAAAGATCGCGAAAGGAGTTAGACAAGGGGATACAATCTCCCCCAANCTATTTANAGCAAGCCTAGNAAGCATATTCCGTAAGACAGATTGGGAGGGAAAGGGGAACTGTCTCTTATACACATC + A#AAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE#EEEEEEE#AEEEEEEEEEE#EEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE @NDX550293_RUO:84:HCCHVBGXJ:1:11101:11299:1046 1:N:0:TATGCCTTAC+TAATGTGTCT GCCCTAGGTATATGTATTCGTCTACCTCTTCTAGTGTCTCTCCGTCAATTTTAATGGCTTGCGAAGGGACTNTGTCATTNAACATTATTTTTGTTTTAGTTTTATTCATCTTAAGACCCACTTTTGTACTTTCTCTATTTAGGTCAGTT + AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE#EEEEEEE#EEEEEEAEEEEEEAEEEEEEEEEEEEEAEEEEEEEEAAAEAEEEEEEEAEEEAAAEEEEEEEEEAEEAA @NDX550293_RUO:84:HCCHVBGXJ:1:11101:15038:1047 1:N:0:TATGCCTTAC+TAATGTGTCT CCTTAACCCTACGGCCATGCGATTTTTCCCACATTCTGATACGTTTTTTGAATATTTTTAGCGGCTCTGGANTAAGTTTNCTTGTGCACGACAGTATGTAAACAGAAATGGTAATTGATACCGACAGAGTGGGGTTTTCTTTTTGAGTG + AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE#EEEAAEE#EEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEAEEEEEAEEEEEEEEEEEEEEEEEEEEA

A_R2:

@NDX550293_RUO:84:HCCHVBGXJ:1:11101:19307:1038 2:N:0:TATGCCTTAC+TAATGTGTCT TTCCCCTTTCCCTCCCAATCTGTCTTACGGAATATGCTTTCTAGGCTTGCTGTANATAGTTTGGGGGAGATTGTATCCCCTTGTCTAACTCCTTTCGCGATCTTTATTTCGTTTGTGTCTCTGTGTAATCTCTGTCTCTTATACACATC + AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE6#EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEAEEEEEEEAAAAEEEEEEAAAAAAEAEAEAAAAAEE/ @NDX550293_RUO:84:HCCHVBGXJ:1:11101:11299:1046 2:N:0:TATGCCTTAC+TAATGTGTCT AGGGGGGGAAAGGGGATAAACATAGACGGGGAATATTTAAACCATATAAGATTCNCCGATGACATATCCACTACTACAGAGACTCCAGTAGAACTACAACAATTGCTAACTGACCTAAATAGAGAAAGTACAAAAGTGGGTCTTAAGAT + AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE#EEEAEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEAEEEEEEEEEEE<EEEEEEEEEEEEAEAEEEEEEEEE @NDX550293_RUO:84:HCCHVBGXJ:1:11101:15038:1047 2:N:0:TATGCCTTAC+TAATGTGTCT GATCGTTTGAGCTTTACAATTTGAATAAAAAATTATGCTAATTAATAACAAAAANCAAATTAATTAGGATAAGTTTCGCTTAATCATGCACTCAAAAAGAAAACCCCACTCTGTCGGTATCAATTACCATTTCTGTTTACATACTGTCG + AAAAAEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEE#EEEEEEEAEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEE/EEAEAAEEEA<EEEAEEAEAEAEEAE<AAAA<A<AAEEEAEEE<AA

B_R1: @NDX550293_RUO:72:HCGVHBGXJ:1:11101:26652:1158 1:N:0:3 AGATAATAGAAGAGACTATTAAAAAAGGGAAAGGTCTAAAGAAAGCTCGGACAATAGAACAAATAGGAAAACAACAAATGC + AAAAAEEEEEEEAEAE/EEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEE/EEEE/EE @NDX550293_RUO:72:HCGVHBGXJ:1:11101:10713:1185 1:N:0:3 TATGGGTGGGGAGTGAGATAGATAGATAGATAGATCTATATAGAGAGAGATTGGGAGAGAGAGAGAGGGGGAGAGAGAGGAATAAAGTGAGTCTTTTTGTAAGGTTCCCACGAGGTTTAATACCAATGTTAATTGATATATTAAGTTTT + AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEAEEEEEEEEEEEEEAA</EEEEEEEEEEEEE<A/AAEEEE<EEE<AEEEE<AAEE// @NDX550293_RUO:72:HCGVHBGXJ:1:11101:12151:1211 1:N:0:3 GGTCTAGACATGTCTATATGTAGACATTCCTATAATGGCAATACTCCTAGCTAAGTGTTAACAGTCAGTGAAGGGGAGAGAGATATGATAATGTGAGTGCAGTGGGAGTCAGCAGTTTTAATAATGATATGGAGAGAAAAGAAGGAAGG + AAAAAEE6EEEEEEEEEEEEEEEEAEEEE<///E/EEEEEEEEEEAA<EEEEEEEE<EEE/EAEEEEEEEEEEEEEE<EAEEE/EEEEEAEEEEEEEEEEEEEEEE<EEAEEE//<AAEEE/EE/EE/EEEEEEEEEE//AEEAE<EE<

B_R2: @NDX550293_RUO:72:HCGVHBGXJ:1:11101:26652:1158 2:N:0:3 GCATTTGTTGATTTCCTATTTGTTCTATTGTCCGAGCTTTCTTTAGACCTTTCCCTTTTTTAATAGTCTCTTCTATTATCT + /AAAA/E/EE////EEEEA<EEEEEEAE/A/AE/EEEE6<AA/EEEAEA///EE<6EEEEE/EEE//</EE/EA/E//E</ @NDX550293_RUO:72:HCGVHBGXJ:1:11101:10713:1185 2:N:0:3 CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAACCTAACCCTAAACCTAAACCAAAAACAAAACCGAAAGAGAATACTATAAAAAAGGAGAAAAAAAAAGAAAAATAAAAAGTAAAACTAAAAGTAGAAAAACTAGAGG + AAAAAEEEEEEEEEEEEAEEEEEAEEEEEEE/EEEE/AEEAE/EAE/E//E//E/<//////A/<///A/////6///////////////////////////////////////////////////////////<////////////// @NDX550293_RUO:72:HCGVHBGXJ:1:11101:12151:1211 2:N:0:3 ATATAAGTCCTCATAGTATGTTGCTACTATTTTTAGTAATTGGTCTCTACATGTGCTTGTGTTGTCATATTTGTCCTTTAGTGTTTGCATCTGTTGTTTTCCTATTTGTTCTACTTTTTTAAGACCTTCCCCTTCCCCTTCCTTCTTTT + AAAA6EEEAEEEEEEEEEE6EEEEAAEE/EEEEE/EA/EE6EEEEA/EE<A6AEE<EEEEEEE/EEAEEEEEEEEEE<AAEEEEEEEAAE/EEEE/E<AEA/AEEEE<E<<AE<AEAAEAAEEEEEEEA/AEE/AA6AEAAAE6AAAEE

Nov 03 '21 09:11 karl1926

Hi,

Yes tha is because of the id structure, but I think I can fix it with an adjustment in the code Will test it tomorrow and let you know

Nov 07 '21 22:11 ndierckx

thank you Nicolas! Keep me posted please!

Karl

Nov 08 '21 08:11 karl1926

Hi, I tried with the reads you send me, but for me it works

Have you checked if there is a empty line at the end of the first file? Then you need to remove it

Could you send the log file? Does it mention 100% subsampled ?

Nov 09 '21 14:11 ndierckx

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INVALID SEED, PLEASE TRY AGAIN WITH A NEW ONE

Project:

Dataset 1:

Heteroplasmy:

Optional:

NOVOPlasty: The Organelle Assembler Version 4.3.1 Author: Nicolas Dierckxsens, (c) 2015-2020

Project:

Dataset 1:

Heteroplasmy:

Optional:

R1 reads

R2 reads

Seed 1

Seed 2

Seed 3

Reference

NOVOPlasty
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