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chenzixi07

multimotifmaker's Issues

I use MultiMotifMaker for identifying motifs but get nothing

Hi, there
I tried MultiMotifMaker for identifying motifs but get no results. Here's is my fasta file and gff file produced from ipdsummary:

>scaffold00014
TTTTACTATTATCGGAAAGTTAATCTTACTTCTTCCTAATATATTATATAATCTTAATAA
ACGTTATTCCCTTAGCTATATTATCTTTATAAATAGCTGAATAAAGTATCTATTATCTTT
ATTAATATAGATAATAATATTTATAACTTTCTCTTCCTCCTTAAAGCTAGCTAAGTAATA
AATATCTTTATTAATTAATTAAGAACTCCTAGAAATTATCCCCTATAAACCTAAAAGCAC
TATTTAACTTTAATATTAATATTATCGCTAATCCCTTATTATTTATTACCTTCTTAAGGA
TATTTTCGAGGATTAATATAAATTAATTAAAAGAAAGGCCTTAAATCGGGATATACTATA
CCTCTCAAGTAAATAGGTAATTAATTATATTCTTATAAAGTACTATTCTAGGTTAAAGAG
GTTAAATATTCTTATAAACTAGTAGGAAAATAGGTCTTAGAGGCCGGCTATTATTAAGAA
GGAGTCTAACTTTATTATCGTTATTATATTAAAGTAGAGAGGGTTAGAAATAGGCGAGGA
TTTACTATCTTTACGAGAATGCTCCCTATAAATAGTAAAAGCCCCTTTTATAAATAAACT
TAGGTATTAGCTATAGTAAATATAGGTTTATTCTCTTAATTAATTAATATAAGGGTTCCG
AGGCTAGATTATTTACTTTACTTTCTTTAATTATTAATTAGGGTCTATCGTTTATTATTA
TTTCTTATTATTTTATTTTATATATATTAATTTTTACTAAGGAAGAAGGGGGGTTATAGA
AGAGGGAGGTCGAAGCTATTTTTAAGGAATCGAGTCGCTTTATATAAGCTTCGCTATAGC
CTCCCCTATCTTAGTATTATATAACCTATTATAGGGTCCTAATACTATAATTAGGGGAAT
ATAATTATTATAGATTAATTATATTATATATATAGCTAGTTAGCTATATATATTATTTAT
ATATAAAGCTTATCTATTATTTATATTATTTATATATAAAGCTTATCTATTATTTATATT
ATTTATATATAAAGCTTATCTATTATTTATATTATTTATATTATATATATAGCTAATTAG
CTATATATATTATTCGTAAATCTCGTATATTTTATAAAATTATAGTATTACTTTAGTAAT
.....

gff file:

##gff-version 3
##source ipdSummary v2.0
##source-commandline /home/sujitmaiti/miniconda3/envs/kinectictools/bin/ipdSummary ../raw.merged.bam --reference ./scaffolds.reduced.fa --gff basemods.gff --csv ki
netics.csv --bigwig IpdRatio.bw --identify m6A,m4C --methylFraction --numWorkers 10 --pvalue 0.01 --minCoverage 3
##sequence-region scaffold00014 1 418576
##sequence-region scaffold00015 1 394874
##sequence-region scaffold00016 1 350982
##sequence-region scaffold00017 1 156563
##sequence-region scaffold00010 1 1520983
##sequence-region scaffold00011 1 1050304
##sequence-region scaffold00012 1 933454
##sequence-region scaffold00013 1 900483
##sequence-region scaffold00018 1 123238
##sequence-region scaffold00019 1 83344
##sequence-region scaffold00024 1 11475
##sequence-region scaffold00007 1 2329946
##sequence-region scaffold00006 1 3148538
##sequence-region scaffold00009 1 1587396
##sequence-region scaffold00008 1 3559532
##sequence-region scaffold00023 1 14512
##sequence-region scaffold00003 1 6610137
##sequence-region scaffold00002 1 8563036
##sequence-region scaffold00001 1 17280981
##sequence-region scaffold00004 1 3506857
##sequence-region scaffold00021 1 42785
##sequence-region scaffold00020 1 47391
##sequence-region scaffold00005 1 2967496
##sequence-region scaffold00022 1 15686
scaffold00014   kinModCall      modified_base   5013    5013    27      -       .       coverage=5;context=ACGCCGGCGCCCAGACCGAGGCCGCGCTCGCCGTGTACCGG;IPDRatio=2.09
scaffold00014   kinModCall      modified_base   5748    5748    21      +       .       coverage=6;context=GGGCGTCCGACATGGCGAGCAGCCAGGGTGGTCGTTCGAGG;IPDRatio=2.16
scaffold00014   kinModCall      modified_base   7639    7639    21      -       .       coverage=13;context=AGGCCGTGCGCGCCATCGGCCGGTGTGCGCAGGCCGATGCG;IPDRatio=3.71
scaffold00014   kinModCall      m4C     14765   14765   20      +       .       coverage=11;context=TAGATATACTCTAAACTAAACTATAGATCGACGAAGTACTC;IPDRatio=1.96;frac=1.000;fracLow=0.367;fracUp=1.000;identificationQv=3
scaffold00014   kinModCall      m6A     16816   16816   23      +       .       coverage=16;context=GTCCGATTAAGAGGAAATCGACTTACTCTTAATAGCTAGAG;IPDRatio=2.67;frac=0.814;fracLow=0.347;fracUp=1.000;identificationQv=8
scaffold00014   kinModCall      m4C     19652   19652   22      -       .       coverage=18;context=GTTCATGCCGGCATAGACGTCCTGGGTAGCTTTCTTCATAT;IPDRatio=1.94;frac=1.000;fracLow=0.728;fracUp=1.000;identificationQv=4
scaffold00014   kinModCall      modified_base   19967   19967   23      +       .       coverage=23;context=AGTATGAACGCAGGATGGAGAAGGGACGAAAGCCCGCCGCA;IPDRatio=3.11

And this is my running

java -jar ~/biosoftware/MultiMotifMaker/artifacts/MultiMotifMaker.jar find -f /home/sujitmaiti/ver/vlgenome/quickmerge/ca_ne/redundans/scaffolds.reduced.fa -g basemods.gff -o motif.csv -t 12

Any help would be appreciated.
Fei

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