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lpenguin / phigaro

Phigaro is a scalable command-line tool for predictions phages and prophages from nucleid acid sequences (including metagenomes) and is based on phage genes HMMs and a smoothing window algorithm.
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GeneMark.hmm 400-day license #5

Open cmajones opened 6 years ago

cmajones commented 6 years ago

Hi there,

I installed phigaro as directed and after running my first command got this error:

`phigaro -f ../virfinder/scaffolds.fasta -o phigaro_out -t 20 Traceback (most recent call last): File "/usr/local/bin/phigaro", line 11, in sys.exit(main()) File "/usr/local/lib/python2.7/dist-packages/phigaro/cli/batch.py", line 118, in main task_output_file = run_tasks_chain(tasks) File "/usr/local/lib/python2.7/dist-packages/phigaro/batch/runner.py", line 18, in run_tasks_chain task.run() File "/usr/local/lib/python2.7/dist-packages/phigaro/batch/task/gene_mark.py", line 29, in run self.gene_mark(self.input) File "/usr/local/lib/python2.7/dist-packages/sh.py", line 1427, in call return RunningCommand(cmd, call_args, stdin, stdout, stderr) File "/usr/local/lib/python2.7/dist-packages/sh.py", line 774, in init self.wait() File "/usr/local/lib/python2.7/dist-packages/sh.py", line 792, in wait self.handle_command_exit_code(exit_code) File "/usr/local/lib/python2.7/dist-packages/sh.py", line 815, in handle_command_exit_code raise exc sh.ErrorReturnCode_1:

RAN: /home/casey/local/MetaGeneMark_linux_64/mgm/gmhmmp -A proc/gene_mark/scaffolds-7e52b7413bc44ee6b22a6a38e45cea72.faa -m /home/casey/local/MetaGeneMark_linux_64/mgm/MetaGeneMark_v1.mod ../virfinder/scaffolds.fasta

STDOUT:

STDERR: GeneMark.hmm 400-day license. Your 400-day license period has ended. We hope that you found this software useful. If you would like to renew this license, please contact GeneProbe, Inc. at custserv@genepro.com`

Let me know if this is an installation issue or if I need to obtain a copy of GeneMark.hmm.

Thanks!

bobeobibo commented 6 years ago

Hi. Did you download MetaGeneMark from http://topaz.gatech.edu/Genemark/license_download.cgi ? If so, you shouldn't receive this message, normally. However, we are planning an update that will avoid using MetaGeneMark and therefore their license issues.

cmajones commented 6 years ago

Hi there, yes I used that link and installed as indicated in the mgm download.

ACPortmann commented 4 years ago

Hi @bobeobibo,

According to your last year post, you were planning an update to avoid using MetaGeneMark:

Hi. Did you download MetaGeneMark from http://topaz.gatech.edu/Genemark/license_download.cgi ? If so, you shouldn't receive this message, normally. However, we are planning an update that will avoid using MetaGeneMark and therefore their license issues.

When do you plan to release this update of phigaro?

Many thanks in advance for your answer.

bobeobibo commented 4 years ago

Hi @ACPortmann , The updated version of Phigaro can be found here https://github.com/bobeobibo/phigaro We don't use mgm anymore.

Thanks for your interest in Phigaro :)