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mjsull / Easyfig

Development version of Easyfig
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Problem in drawing figure #18

Open romen86 opened 5 years ago

romen86 commented 5 years ago

I would like to analyze 10 prophage genomes (gbk format) and each gbk file has ~120kb. I added a colour feature to each gbk file manually, say, /colour=7 based on the genbank file provided in the example. The blastn output files generated well, however, when I clicked the create figure section, it takes very long time and the figure was not generated. I don't really know that whether the program on the progress or struck or it doesn't prompt any error messages too. What will be the possible reasons for this troubleshooting and how can I fix this issue? Please help!!

luongphekidz07 commented 5 years ago

Hello, I am Le Phuong, currently, I am having the trouble with Easyfig, I can not change the color for the specific genes in Easy. When you have time, could you tell me how I can do it manually? Thank you very much,

romen86 commented 5 years ago

Hello Le Phuong, I figure out the issue while drawing colour code for the specific gene. For Example: CDS 548..1435 /gene="xoxo" /locus_tag="LGMCDKNP_00002" /inference="ab initio prediction:Prodigal:2.6" /inference="similar to AA sequence:RefSeq:YP_005744820.1" /codon_start=1 /transl_table=11 /product="recombinase" /colour=16 /translation="METIIEEYLRFIQIEKGLSSNTIGAYRRDLKKYQDYM IDFIDRQLIQECLGHNGYRDRTMLELLYATGMRVSELIHLELENVNL IMGFVRVFGKGDKERIVPLGDAVIETVTEVLFLNMHGKPLSR THV QAIWKMIKQNHSFATHLLENGADLRAVQEMLGHSDISTTQLYRH SQIRKMYNQFHPRA" After /product="site-specific recombinase XerD", Use Enter Key to begin new line and press SpaceBar to reach and write /colour=16. Note: Please do not use any Tab from the keyboard. Always use Spacebar while adding colour to the next line.

luongphekidz07 commented 5 years ago

Hello Romen, Thank you very much for your nice repsonse, I followed your recommendations but I failed. Anyways, thank you very much for your help

mjsull commented 5 years ago

Hi Le Phuong,

Make sure you only use spaces and also each line must be indented by the right amount using only spaces. Have a look at the example files for a guide.

Best,

Mitch

luongphekidz07 commented 5 years ago

Hello Mitch,

Thank you very much for your help, I will try again,

Yours sincerely, Le Phuong.

J-Chunyu commented 4 years ago

Hello, I am a novice in bioinformatics, and recently I have encountered some problems in the annotation of phages. May I ask which database is suitable for the annotation of phages？

romen86 commented 2 years ago

Hi, This question is beyond the issues of this software. However, as far as my knowledge you can use PHASTER webtool or Patric webserver.

claire-elek commented 1 year ago

Hi, I'm also having the same problem as romen86.

Easyfig gets stuck drawing figure. The blast .out files are generated, but the program just stops working at "drawing figure." I have been looking for a solution and asking questions for months now. Initially Easyfig worked fine on my Windows machine. I didn't change anything at all, and one day it just no longer worked.

This issue was first reported in 2018, it's now 2022. Does anyone have or know of a fix for this problem?

DAFO7368 commented 1 year ago

I'm having the sameproblem. Easyfig gets stuck drawing figure, Has anyone solved the problem ?