Failure during iterations

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david....@googlemail.com

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Nov 28, 2016, 6:24:16 PM11/28/16

to EMIRGE users

Hi,

I've been trying out EMIRGE on a number of datasets. When applied to SRR4381491, EMIRGE fails at iteration 4. Looking at the results at the earlier iterations, something strange appears to be happening. A typical example is shown below:-

At iteration 2,
>KC671266.1.1815
ANNCNGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTATAAAC
AAATTTGTACTGTGAAACTGCGAATGGCTCATTAAATCAGTTATAGTTTATTTGATGGTA
CCTTGCTACATGGATAACTGTGGTAATTCTAGAGCTAATACATGCAATCAAGCCCCGACT
TCTGGGAGGGGTGTATTTATTAGATAAAAAACCAACGCGGCTTGCCGCTCGTTTGGTGAT
TCATAATAACTTCTCGAATCGCATGGCCTTGTGCCGGCGATGCTTCATTCAAATATCTGC
CCTATCAACTTTCGATGGTAGGATAGTGGCCTACCATGGTTTCAACGGGTAACGGGGAAT
AAGGGTTCGATTCCGGAGAGGGAGCCNGAGAAACGGCNACCACANCCAAGGAAGGCAGCA
GGCGCGCAAANNACCCAANCCCGACACGGGGAGGNAGNGACAANAAANGACAANACAGGG
CNCNNNNGGGNCCNGNAANNGGAANGAGNACAANNNAAANCCCNNAACGAGGAACAANNG
GAGGGCAAGNCNGGNGCCAGCAGCCGCGGNAANNCCAGCNCCAANAGCGNANANNAAAGN
NGNNGCAGNNAAAAAGCNCGNAGNNGAACNNCAGGCCNGGCCGGGCGGNCCGCCNAACGG
CGTGTACTGTCTGGCTGGGTCTTACCTCTTGGTGAACTTGCATGCCCTTCACTGGGTGTG
TAAGGGAACCAGGACTTTTACCTTGAGAAAATTAGAGTGTTCAAAGCAGGCCTACGCCCG
AATACATTAGCATGGAATAATAGAATAGGACGTGCGGTCCTATTTTGTTGGTTTCTAGGA
TCGCCGTAATGATAAATAGGGACAGTTGGGGGCATTTGTATTGCGTCGCTAGAGGTGAAA
TTCTTGGATTGACGCAAGACAAACTACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAA
TCAAGAACGAAGGTTAGGGGATCGAAAACGATCAGATACCGTTGTAGTCTTAACAGTAAA
CTATGCCGACTAGGGATCGGGCGATCTCACTTTTATGTGTCGCTCGGCACCTTACGAGAA
ATCAAAGTCTTTGGGTTCTGGGGGGAGTATGGTCGCAAGGCTGAAACTTAAAGGAATTGA
CGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGGAAACTC
ACCAGGNCCAGACANAACNAGGATTGACAGATTGATAGCTCTTTCTTGATTCTATGGGTG
GTGGTGCATGGCCGTTCTTAGTTGGTGGAGTGATTTGTCTGGTTAATTCCGATAACGAAC
GAGACCTTAACCTGCTAAATAGTCAGGCCGGCTTTTGCTGGTCGCGGACTTCTTAGAGGG
ACTGTCGGCGTCTAGCCGACGGAAGTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGAT
GTTCTGGGCCGCACGCGCGCTACACTGACAGAGCCAGCGAGTTTTTTTCCTTGGCCGAAA
GGTCTGGGTAATCTTGTGAAACTCTGTCGTGCTGGGGATAGAGCATTGCAATTATTGCTC
TTCAACGAGGAATACCTAGTAAGCGTGAGTCATCAGCTCGCGTTGATTACGTCCCTGCCC
TTTGTACACACCGCCCGTCGCTACTACCGATTGAATGGCTTAGTGAGATCTCCGGATTGG
CTTCGGGGAGCCGGCAACGGCACCCTGTCGCTGAGAAGCTGGTCAAACTTGGTCATTTAG
AGGAAGTAAAAGNCGNAACAAAGGGCGANNCGCGGCCGC

At iteration 3, this candidate becomes:-
>KC671266.1.1815
ANNCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNCNGAGAAACGGCNACCACANCCAAGGAAGGCAGCA
GGCGCGCAAANNACCCAANCCCGACACGGGGAGGNAGNGACAANAAANGACAANACAGGG
CNCNNNNGGGNCCNGNAANNGGAANGAGNACAANNNAAANCCCNNAACGAGGAACAANNG
GAGGGCAAGNCNGGNGCCAGCAGCCGCGGNAANNCCAGCNCCAANAGCGNANANNAAAGN
NGNNGCAGNNAAAAAGCNCGNAGNNGAACNNCAGGCCNGGCCGGGCGGNCCGCCNAACNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNC
ACCAGGNCCAGACANAACNAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNCGNAACAAAGGGCGANNCGCGGCCGC

It is as if it discarded the iteration 2 sequence and substituted it with some new sequence where iteration 2 had some Ns. The run then terminates abnormally at iteration 4.

EMIRGE ran fine on SRR4381490 and SRR4381492. Paired end reads were filtered and primers removed prior to EMIRGE. Could you tell me how to fix this?

Thanks,
David

spongebob

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Feb 20, 2019, 2:44:56 PM2/20/19

to EMIRGE users

Hi david,

Did you ever solve this? I have the same issue myself.

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