PR2 database

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Ulrike Obertegger

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Mar 24, 2017, 3:34:12 AM3/24/17
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Dear MICCA users,


this was my last try to make MICCA work with the PR2 database:

I loaded as input the OTU file of the mwanihana example datafile. MICCA executes the command, but again, the output I get is "unclassified" for all 1342 OTUs.

Here the command lines I used + the head of those files


who can help?


best regards,

Ulrike


pr2_ref=PR2_database/pr2_gb203_version_4.5.fasta


pr2_tax=PR2_database/pr2_gb203_version_4.5.taxo


micca classify -m cons --cons-threads 10 --cons-maxhits 5 --cons-id 0.9 -i denovo_greedy_otus/otus.fasta -o taxa_pr2.txt --ref $pr2_ref --ref-tax $pr2_tax



head PR2_database/pr2_gb203_version_4.5.taxo

GU824834.1.1056_U Eukaryota;Alveolata;Alveolata_X;Alveolata_XX;Alveolata_XXX;Alveolata_XXXX;Alveolata_XXXXX;Alveolata_XXXXX_sp.;

FJ911926.1.909_U Eukaryota;Alveolata;Alveolata_X;Alveolata_XX;Alveolata_XXX;Alveolata_XXXX;Alveolata_XXXXX;Alveolata_XXXXX_sp.;

GU823937.1.1056_U Eukaryota;Alveolata;Alveolata_X;Alveolata_XX;Alveolata_XXX;Alveolata_XXXX;Alveolata_XXXXX;Alveolata_XXXXX_sp.;

GU824317.1.1056_U Eukaryota;Alveolata;Alveolata_X;Alveolata_XX;Alveolata_XXX;Alveolata_XXXX;Alveolata_XXXXX;Alveolata_XXXXX_sp.;

GU823858.1.1056_U Eukaryota;Alveolata;Alveolata_X;Alveolata_XX;Alveolata_XXX;Alveolata_XXXX;Alveolata_XXXXX;Alveolata_XXXXX_sp.;

GU824316.1.1370_U Eukaryota;Alveolata;Alveolata_X;Alveolata_XX;Alveolata_XXX;Alveolata_XXXX;Alveolata_XXXXX;Alveolata_XXXXX_sp.;

GU824094.1.1180_U Eukaryota;Alveolata;Alveolata_X;Alveolata_XX;Alveolata_XXX;Alveolata_XXXX;Alveolata_XXXXX;Alveolata_XXXXX_sp.;

GU824585.1.1181_U Eukaryota;Alveolata;Alveolata_X;Alveolata_XX;Alveolata_XXX;Alveolata_XXXX;Alveolata_XXXXX;Alveolata_XXXXX_sp.;

GU824593.1.1180_U Eukaryota;Alveolata;Alveolata_X;Alveolata_XX;Alveolata_XXX;Alveolata_XXXX;Alveolata_XXXXX;Alveolata_XXXXX_sp.;

DQ103802.1.1629_U Eukaryota;Alveolata;Alveolata_X;Alveolata_XX;Alveolata_XXX;Alveolata_XXXX;Alveolata_XXXXX;Alveolata_XXXXX_sp.;



head PR2_database/pr2_gb203_version_4.5.fasta

>GU824834.1.1056_U

CGGTAATTCCAGCTCCAATAGCGTATGCTAAAATTGTTGCGGTTAAAACGCTCGTAGTTGTACGTTCCTCCAGGGCACTCGGATTTTTCGTACAGAAGGTTCCGAGTGGTCTGTGAAATTATCTTACAAAGCGGTCTCTTGCTGAGCACGCGGAAAGGGATACTTGTACCTTGAAGAAATTAGAGTGCTTCAAGCAGATTATTGTCTGAATATTATAGCATGGAACAGTTGGAGAAGACACTGGTTCTATTAGAGATTTGTAGAGCAGGTGTAATAGTTGAGAGGAACAGAAGGGGGCATTCATATTCGCATGTGAGAGGTGGAATTCTTGGATCTTGCGAAGGTGGACTACTGCGAAAGCATTTGTCAAGAATGTTTTCATTAATCAAGAACGAAAGTTAGGGGATCGAAGACGATTAGATACCGTCCTAGTCGTAACCATAAACCATGCCTTTTGGAGATCAGGTGAACCTCGAACGCAGAGGATTCTGGCATCCTAGGGGAAACTAAAATTTTTGGGTTCCGGGGGGAGTATGGTCGCAAGACTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCTTGCGGCTTAATTTGACTCAACGCGAGAAATCTCACCAGGTCCAGACATGGGAAGGATTGACAGAGAAGCAGCTTTTTCTCGATTACATGGGTGGTGGTGCATGGCCGTTCTCAGTTGGTGGGGTGATCTGTCTGGTTGATTCCGATAACGAACGAGACCTCGACCTACTAAATAATTAGCACTTTGCTGTAAGTGATGATTTCTTAGAGGGACTTTTCGTGTCCAACGAAAGGAAGTATGAGGCTATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCTGCACGCGCGCTACACTGACATAGACAGAGAGATGTTCCTATCCGAGGGGAGTGGAGAAACTTGAGAGGGTATGTCGTGATGGGGATAGTTTATTGCAATTATTGAACTTAAACGAGGAATTCCTAGTAAGCGTATGGAATGAACTTACGCTGATTACGTCCCTGCCCTTTGTACACACCGCCC

>FJ911926.1.909_U

TCTGCCGTCAGGTGTGTACTGGCAGTGTTTGGCATCTATTCGAGATTGGGTGTCCACTTGATTGTGTGCACTCGATGTCGGAGCTAATACTTTGAGAAAATTAGAGTGTTCCACGCAGGCGCGTGCCTTGAATACTGCAGCATGGGATATTGGAAGGCCGATTGAGCTTTCTTGTTGGTTCTCGGTTTGATCGGAATGATTAATAGGGATAGTTGGGGGCATTCGTATTCAACTGTCAGAGGTGAAATTCTTGGATTTGTTGAAGACGGACTACTGCGAAAGCATCTGCCATGGATGTTCTCATTGATCAAGAACGAAAGTTAGGGGATCGAAGACGATCAGATACCGTCCTAGTCTTAACCATAAACTATCTCGACTAGGGATTGGAGGCCGTTACTTCTACGACTCCTTCAGCACCTTATGGGAAACCAAAGTCTTTGGGGTCTGGGGGGAGTATGGTCGCAAGGCTGAAACTTAAAGGAATTGACGGGAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAAACTCACCAGGTCCAGACATGGTAAGGATTGACAGATTGAAAGCTCTTTCTTGATTCTATGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGTGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTTGGCCTGCTAAATAGACACTGTCTCCTCGGAGGCAGGCTGCTCTTCTTAGAGGGACTCAGCGAATCTATCGCTGGGAAGTGCGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCTGCACGCGCGCTACACTGATGCACTCAACGAGTTTACAACCTTATCCGGAAGGATTGGGTAATCTTTTGAACGTGCATCGTGATGGGGATAGATTATTGCAATTATTAATCT

>GU823937.1.1056_U

CGGTAATTCCAGCTCCAATAGCGTATGCTAAAATTGTTGCGGTTAAAACGCTCGTAGTTGTACGTTCCTCCAGGGCACTCGGATTTTTCGTACAGAAGGTTCCGAGTGGTCTGTGAAATTATCTTACAAAGCGGTCTCTTGCTGAGCACGCGGAAAGGGATACTTGTACCTTGAAGAAATTAGAGTGCTTCAAGCAGATTATTGTCTGAATATTATAGCATGGAATAGTTGGAGAAGACACTGGTTCTATTAGAGATTTGTAGAGCAGGTGTAATAGTTGAGAGGAACAGAAGGGGGCATTCATATTCGCATGTGAGAGGTGGAATTCTTGGATCTTGCGAAGGTGGACTACTGCGAAAGCATTTGTCAAGAACGTTTTCATTAATCAAGAACGAAAGTTAGGGGATCGAAGACGATTAGATACCGTCCTAGTCTTAACCATAAACCATGCCTTTTGGAGATCAGGTGAACCTCGAACGCAGAGGATCCTGGCATCCTAGGGGAAACTAAAATTTTTGGGTTCCGGGGGGAGTATGGTCGCAAGACTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCTTGCGGCTTAATTTGACTCAACGCGAGAAATCTCACCAGGTCCAGACATGGGAAGGATTGACAGAGAAGCAGCTTTTTCTCGATTACATGGGTGGTGGTGCATGGCCGTTCTCAGTTGATGGGGTGATCTGTCTGGTTGATTCCGATAACGAACGAGACCTCGACCTACTAAATAATTAGCACTTTGCTGTAAGTGATGATTTCTTAGAGGGACTTTTCGTGTCCAACGAAAGGAAGTATGAGGCTATAACAGGTCTGTGATGCCCTTAGATGTCCTGGGCTGCACGCGCGCTACACTGACATAGACAGAGAGATGTTCCTATCCGAGGGGAGTGGAGAAACTTGAGAGGATATGTCGTGATGGGGATAGTTTATTGCAATTATTGAACTTAAACGAGGAATTCCTAGTAAGCGTATGGAATGAACTTACGCTGATTACGTCCCTGCCCCTTGTACACACCGCCC

>GU824317.1.1056_U

CGGTAATTCCAGCTCCAATAGCGTATGCTAAAATTGTTGCGGTTAAAACGCTCGTAGTTGTACGTTCCTCCAGGGCACTCGGATTTTTCGTACAGAAGGTTCCGAGTGGTCTGTGAAATTATCTTACAAAGCGGTCTCTTGCTGAGCACGCGGAAAGGGATACTTGTACCTTGAAGAAATTAGAGTGCTTCAAGCAGATTATTGTCTGAATATTATAGCATGGAATAGTTGGAGAAGACACTGGTTCTATTAGAGATTTGTAGAGCAGGTGTAATAGTTGAGAGGAACAGAAGGGGGCATTCATATTCGCATGTGAGAGGTGGAATTCTTGGATCTTGCGAAGGTGGACTACTGCGAAAGCATTTGTCAAGAATGTTTTCATTAATCAAGAACGAAAGTTAGGGGATCGAAGACGATTAGATACCGTCCTAGTCTTAACCATAAACCATGCCTTTTGGAGATCAGGTGAACCTCGAACGCAGAGGATTCTGGCATCCTAGGGGAAACTAAAATTTTTGGGTTCCGGGGGGAGTATGGTCGCAAGACTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCTTGCGGCTTAATTTGACTCAACGCGAGAAATCTCACCAGGTCCAGACATGGGAACGATTGACAGAGAAGCAGCTTTTTCTCGATTACATGGGTGGTGGTGCATGGCCGTTCTCAGTTGGTGGGGTGATCTGTCTGGTTGACTCCGATAACGAACGAGACCTCGACCTACTAAATAATTAGCACTTTGCTGTAAGTGATGATTTCTTAGAGGGACTTTTCGTGTCCAACGAAAGGAAGTATGAGGCTATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCTGCACGCGCGCTACACTGACATAGACAGAGAGATGTTCCTATCCGAGGGGAGTGGAGAAACTTGAGAGGATATGTCGTGATGGGGATAGTTTATTGCAATTATTGAACTTAAACGAGGAATTCCTAGTAAGCGTATGGAATGAACTTACGCTGATTACGTCCCTGCCCCTTGTACACACCGCCC

>GU823858.1.1056_U

CGGTAATTCCAGCTCCAATAGCGTATGCTAAAATTGTTGCGGTTAAAACGCTCGTAGTTGTACGTTCCTCCAGGGCACTCGGATTTTTCGTACAGAAGGTTCCGAGTGGTCTGTGAAATTATCTTACAAAGCGGTCTCTTGCTGAGCACGCGGAAAGGGATACTTGTACCTTGAAGAAATTAGAGTGCTTCAAGCAGATTATTGTCTGAATATTATAGCATGGAATAGTTGGAGAAGACACTGGTTCTATTAGAGATTTGTAGAGCAGGTGTAATAGTTGAGAGGAACAGAAGGGGGCATTCATATTCGCATGTGAGAGGTGGAATTCTTGGATCTTGCGAAGGTGGACTACTGCGAAAGCATTTGTCAAGAATGTTTTCATTAATCAAGAACGAAAGTTAGGGGATCGAAGACGATTAGATACCGTCCTAGTCTTAACCATAAACCATGCCTTTTGGAGATCAGGTGAACCTCGAACGCAGAGGATTCTGGCATCCTAGGGGAAACTAAAATTTTTGGGTTCCGGGGGGAGTATGGTCGCAAGACTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCTTGCGGCTTAATTTGACTCAACGCGAGAAATCTCACCAGGTCCAGACATGGGAAGGATTGACAGAGAAGCAGCTTTTTCTCGATTACATGGGTGGTGGTGCATGGCCGTTCTCAGTTGGTGGGGTGATCTGTCTGGTTGATTCCGATAACGAACGAGACCTCGACCTACTAAATAATTAGCACTTTGCTGTAAGTGATGATTTCTTAGAGGGACTTTTCGTGTCCAACGAAAGGAAGTATGAGGCTATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCTGCACGCGCGCTACACTGACATAGACAGAGAGATGTTCCTATCCGAGGGGAGTGGGGAAACTTGAGAGGATATGTCGTGATGGGGATAGTTTATTGCAATTATTGAACTTAAACGAGGAATTCCTAGTAAGCGTATGGAATGAACTTACGCTGATTACGTCCCTGCCCCTTGTACACACCGCCC


head denovo_greedy_otus/otus.fasta

>DENOVO1

GACGAACGCTGGCGGCGTGCCTAACACATGCAAGTCGAACGGGGTGAGGCCCTTCGGGACCTCACTTAGTGGCGAACGGGTGAGTAACGCGTGAAGAACCTGCCTTTCAGTGGGGGACAACAGTTGGAAACGACTGCTAATACCGCATAATGTATTTAGGGGGCATCCTCTGGATACCAAAGCTTTATGTGCTGAAAGATGGCTTCGCGTCTGATTAGCTAGTTGGCGGGGTAACGGCCCACCAAGGCGACGATCAGTAGCCGGTCTGAGAGGATGAACGGCCACATTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGGGCAATGGGC

>DENOVO2

GATGAACGCTAGCTACAGGCTTAACACATGCAAGTCGAGGGGCAGCGGGAGCTTAGCTTGCTAAGTTTGCCGGCGACCGGCGCACGGGTGAGTAACACGTATCCAACCTTCCCGTCACTCGGGTATAGCCTTCCGAAAGGGAGATTAATCCCCGATGTAATTATGTTTTCGCATGAGAGTGTAATTAAAGATTAATCGGTGATGGATGGGGATGCGTTCCATTAGCTTGTTGGTGGGGTAACGGCTCACCAAGGCTACGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGAGGAATATTGGTC

>DENOVO3

AGTGAACGCTGGCGACGTGGTTAAGACATGCAAGTCGAGCGGTATTGAAGTTGTAGCAATACAATGGAGAGAGAGCGGCGAACGGGTGCGTAACACGTGAGAAATCTGCCTTGAAGTTTGGAATAGCCCGGGGAAACTCGGATTAATGCCGGATGTGGTGGCGAGCGGCATCGCTTGTCAACTAAAGTTTGAGACGACGCTTCAAGAGGGTCTCGCGGCCTATCAGCTTGTTGGTGAGGTAACGGCTCACCAAGGCGAAGACGGGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGAACTGAGACACGGTCCAGACACCTACGGGTGGCAGCAGTTTCGAATCATTCA

>DENOVO4

GATGAACGCTAGCGACAGGCTTAACACATGCAAGTCGAGGGGCAGCGGGGAAGTAGCAATACTTCTGCCGGCGACCGGCGCACGGGTGAGTAACACGTATGTAACCTGCCCGTAGCAGGGGGATAAGCGGAAGAAATTCCGTCTAATACCGCGTAATAAACTTCGGAGGCATCTTCGGAGTTTCAAAGGAGCAATCCGGCTACGGATGGACATGCGTCGCATTAGTTAGTTGGCGGGGTAACGGCCCACCAAGACGACGATGCGTAGGGGTTCTGAGAGGAAGGTCCCCCACACTGGTACTGAGACACGGACCAGACTCCTACGGGAGGCAGCAGTGAGGAATATTGGTC

>DENOVO5

GATGAACGCTAGCGACAGGCTTAACACATGCAAGTCGAGGGGCAGCGGAGATGTGGCAACACATTTGCCGGCGACCGGCGCACGGGTGAGTAACACGTATGCAACCTGCCCGTCACAGGGGGATAATCGGGAGAAATCCCGTCTAATACCGCGTAACACCTATGGGAGACATCTCTTATGGGTCAAAGGAGCAATCCGGTGACGGATGGGCATGCGTCGCATTAGCTAGTCGGCGGGGTAACGGCCCACCGAGGCGACGATGCGTAGGGGTTCTGAGAGGAAGGTCCCCCACACTGGTACTGAGACACGGACCAGACTCCTACGGGAGGCAGCAGTGAGGAATATTGGTC


Davide Albanese

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May 4, 2017, 4:29:15 AM5/4/17
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