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MGEScan / mgescan

A Galaxy based system for identifying retrotransposons in genome
http://mgescan.github.io/mgescan/
GNU General Public License v3.0
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Empty results #12

Open maybelinot opened 8 years ago

maybelinot commented 8 years ago

Hello @lee212 ,

I've tried to test this tool on some sample input, but didn't achieve positive results (empty ltr.out and ltr.gff3 without any records):

Here is output:

(mgescan)[maybelinot@**** mgescan]$ mgescan ltr ./input_slice_chr6/
MGEScan environment variable is not defined or .mgescanrc is not sourced.
/home/maybelinot/mgescan3 (default path) is used to run MGEScan
==================================================
[Error] matcher is not found. 
==================================================
==================================================
[Error] transeq is not found. 
==================================================
ltr: starting
Returned 0
Finding LTRs
Finding MEM
Making bin
Finding putative ltr
10000   20000   30000   40000   50000   60000   70000   80000   90000   100000  110000  120000  130000  140000  150000  160000  170000  180000  190000  200000  210000  220000  230000  240000  250000  260000  WARNING: no putative LTR in chr6_sliced_q12.fa
Returned 0
Returned 0
ltr: finishing (elapsed time: 45 secs)

input_slice_chr6 folder contains one .fasta file with part of chr6(62,700,001-69,200,000) of GRCh38/hg38, which definitely have LTRs. Probably I have missed some steps via installation(matcher, transeq) not listed in README . Could you help me with this issue?

lee212 commented 8 years ago

EMBOSS is missing on your machine according to your 'matcher' and 'transeq' error messages. If you use Ubuntu, you can install it like: sudo apt-get install emboss -y Let me know if you have any further questions.

maybelinot commented 8 years ago

@lee212, thanks for pointing, missed this step via installation. Works fine now!

I have another one question.. Is there option to predict family of putative LTRs element(Ty3/Gypsy, Bel/Pao, Ty1/Copia for example)?