20 issues in mlin/PhyloCSF
Help on getting multiple alignment for PhyloCSF
Hello Dr. Lin, Thanks a lot for the contribution of PhyloCSF. I'm trying to use PhyloCSF to evaluate the likelihood that some novo ORFs were protein coding. These ORFs were found by performing ORF-RATER ...
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Opened by xlc2015
Aug 6, 2017
[ERROR] No package named ocaml+twt found.
Hi, I'm trying to install PhyloCSF on CentOs 7. When I run : opam install batteries ocaml+twt gsl I get the error: [ERROR] No package named ocaml+twt found. gsl and batteries installed. How can ...
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Opened by shlomita
Jan 31, 2017 - 1 comment
PhyloCSF fails with GSL_exn exception
Run PhyloCSF with parameters "100vertebrates" and the attached 2-codon fasta alignment. chr19-44274475-44274480-.hg38_100.txt It fails with this message: exception 0 5 Error.Gsl_exn(_) failure ...
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Opened by iljungr
Jan 12, 2017
rm: cannot remove './PhyloCSF/src/_build': Directory not empty
I got an mistake after running make . Can anyone help me? I would appreciate it very much. ocamlfind install CamlPaml META _build/CamlPaml.cmi _build/CamlPaml.cma _build/CamlPaml.cmxa _build/CamlPaml.a ...
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Opened by yongjieliu
Dec 27, 2016
ocaml+twt not found
opam install ocaml+twt [ERROR] No package named ocaml+twt found. opam --version 2.0~alpha5 when i use version 1.2.2, it still tell No package named ocaml+twt found.
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Opened by cha1n
Oct 21, 2016 - 3 comments
Issue with completing run
Mike Lin, I have recently downloaded and successfully installed PhyloCSF on Mac OS X Mavericks, however I am having an issue running the program with FASTA alignments I have generated, which I will describe ...
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Opened by jdwheaton
Jul 22, 2014 - 1 comment
How can I check which species are included in the PhyloCSF?
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Opened by Delasa
Apr 4, 2014 - 2 comments
Unbound module Gsl
Dear Mike Lin: I follow the "Obtaining the PhyloCSF software" step on the wiki page,but when I execute make command under PhyloCSF folder,Errors occur: zhangjun@ubuntu:/usr/local/src/PhyloCSF$ ...
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Opened by pingguoilove
Jun 18, 2013 - 20 comments
Fatal error on running PhyloCSF in too old kernel system
Dear Mike Lin, I met a problem when I run PhyloCSF in our linux system. It reported that 'FATAL: kernel too old'. Could you help me how to solve this problem. Many thanks, Jie
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Opened by msswjw
Dec 11, 2012 - 2 comments
I use ocaml 4.00.1 and there are some syntax errors in file /lib/CamlPaml/Expr.ml
line 67-90: | Add (l,r) -> Buffer.add_char b '('; f l; Buffer.add_string b " + "; ...
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Opened by fanzhihang
Nov 22, 2012 - 1 comment