lee212
commented
6 years ago Hi Sam,
It seems tandem repeats finder did not generate any output which prevented further analysis. Sometimes it happens when input sequences are different from what MGEScan LTR expects to process and we may have to look at each step of the program since mgescan uses several tools as a set. Also, I noticed that you ran the program with 1.3.1. There is an updated version which I recommend to use because some issues have fixed. You can download the newest version from here: https://mgescan.readthedocs.io/en/latest/installation.html or from github directly: https://github.com/MGEScan/mgescan
If you could share your input sequence with me probably I can run a test and see where it fails. A single small input sequence would be fine.
Sorry for the late response. And I am communicating with our system team to revive the galaxy web server. It was on a OpenStack virtual machine, and it's currently inaccessible. I might have to update my account to get a new allocation.
Thank you, Hyungro
Hi
MGEScan seems to be a very good tool for TE annotation. When I try to run MGEScan for a plant genome chr 2, it seems that non-LTR prog runs well. But the LTR (find_ltr.pl) provides error output. I just followed the README guidelines. could u please help in fixing this issue.
Report; BnigraV2_genome_B2 Finding LTRs Finging MEM mv: cannot stat
BnigraV2_genome_B2.2.7.7.80.10.50.500.mask': No such file or directory rm: cannot removeBnigraV2_genome_B2.2.7.7.80.10.50.500.dat': No such file or directory Mon Feb 26 11:28:19 2018perl run_MGEScan.pl -genome=~/tools/TE_tools/MGEScan1.3.1/test2/ -data=~/tools/TE_tools/MGEScan1.3.1/t2_ltr_out/ -hmmerv=3 -program=L
On another note - I couldn't get connected to the galaxy server.
Thanks in advance Sam