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Tagliacollo / PFinderUCE-SWSC-EN

New partitioning method for phylogenomic studies of UCEs: Sliding-Window Site Characteristics (SWSC)
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output .csv file empty #3

Open idanaughton opened 5 years ago

idanaughton commented 5 years ago

Hello,

I am not receiving any errors when I run this code with my input file, but my output .csv file is empty. The file simply includes: name,uce_site,aln_site,window_start,window_stop,type,value,plot_mtx, along the top. Anybody else have this issue or know what may be causing it?

Thanks much!

Ida

FanTacyTutu commented 2 years ago

Same problem. I find when input a concatenated matrix, the code can run properly, but when the input is a single UCE locus nexus file, the output will always be empty, both .csv and .cfg. Is it likely that the code had problem with short sequences?

FanTacyTutu commented 2 years ago

it turns out not because of the length of sequences, but the input file must have the string " image " like this ,or like the input example file. BEGIN SETS;

[loci]
CHARSET chr_2828 = 1-376;
CHARSET chr_4312 = 377-627;
CHARSET chr_4575 = 628-1060;
CHARSET chr_4599 = 1061-1474;
CHARSET chr_4660 = 1475-1768;
CHARSET chr_4748 = 1769-2413;
CHARSET chr_4758 = 2414-2695;
CHARSET chr_4790 = 2696-3143;
CHARSET chr_5022 = 3144-3476;
CHARSET chr_5678 = 3477-3948;
CHARSET chr_5708 = 3949-4234;
CHARSET chr_5739 = 4235-4568;
CHARSET chr_1410 = 4569-5031;
CHARSET chr_1600 = 5032-5467;
CHARSET chr_1757 = 5468-5786;

CHARPARTITION loci = 1:chr_2828, 2:chr_4312, 3:chr_4575, 4:chr_4599, 5:chr_4660, 6:chr_4748, 7:chr_4758, 8:chr_4790, 9:chr_5022, 10:chr_5678, 11:chr_5708, 12:chr_5739, 13:chr_1410, 14:chr_1600, 15:chr_1757;

END;