Errors with mcoffee

[moibernabeu]

Hi!

I have two problems that prevent me using mcoffee:

1. TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE pid 57636 ppid 56003. This error appears when I run the command
   $ t_coffee raw_sequences.fa -mode mcoffee
   How can I solve this to use mcoffee?

2. I usually install software in a concrete folder that is in PATH, but, if I try to have alignment programs in this software folder (downloaded from pages that appear at t_coffee introduction) t_coffee does not recognize it. How can I redirect t_coffee to the paths that are stored in .bash_profile (I'm in mac).

[cnotred]

Hello Please send me the sequences to check what be the problem. Send them PM If you use the deafult installer, T-Coffee comes with bundled binaries and you shoudl not use your local versions. If you want to use your own binaries, you must modify your PATH (this is standard UNIX, you can look it up) Typically: 1. Open the . bashrc file in your home directory (for example, /home/your-user-name/. bashrc ) in a text editor. 2. Add*export PATH*="your-dir:$*PATH*" to the last line of the file, where your-dir is the directory you want to add. 3. Save the . bashrc file. 4. Restart your terminal. Bear in mind that binaries will be used in the order in which they are found in the PATH directories, Cheers, Cedric Le 1/9/20 à 11:30, moibernabeu a écrit :

Hi! I have two problems that prevent me using mcoffee: 1. TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE pid 57636 ppid 56003. This error appears when I run the command |$ t_coffee raw_sequences.fa -mode mcoffee| How can I solve this to use mcoffee? 2. I usually install software in a concrete folder that is in PATH, but, if I try to have alignment programs in this software folder (downloaded from pages that appear at t_coffee introduction) t_coffee does not recognize it. How can I redirect t_coffee to the paths that are stored in .bash_profile (I'm in mac). — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#34>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABML3KKTBVJJOKHMX7I7UZ3SDS5MRANCNFSM4QRP472A>.

-- ########################################## Dr Cedric Notredame, PhD Group Leader Notredame's lab - Comparative Bioinformatics Group Bioinformatics and Genomics Programme Room 440.03 Centre de Regulació Genòmica (CRG) Dr. Aiguader, 88 08003 Barcelona Spain Ph# + 34 93 316 02 71 Fax# + 34 93 316 00 99 Mobile# + 34 66 250 47 82 email [email protected] url www.tcoffee.org blog cedricnotredame.blogspot.com ORC-ID: 0000-0003-1461-0988 ###########################################

[moibernabeu]

Here you have the sequences! I have the path this way, at the end of the line… Thanks! Moisès

…

El 1 set 2020, a les 11:34, Cedric Notredame ***@***.***> va escriure: Hello Please send me the sequences to check what be the problem. Send them PM If you use the deafult installer, T-Coffee comes with bundled binaries and you shoudl not use your local versions. If you want to use your own binaries, you must modify your PATH (this is standard UNIX, you can look it up) Typically: 1. Open the . bashrc file in your home directory (for example, /home/your-user-name/. bashrc ) in a text editor. 2. Add*export PATH*="your-dir:$*PATH*" to the last line of the file, where your-dir is the directory you want to add. 3. Save the . bashrc file. 4. Restart your terminal. Bear in mind that binaries will be used in the order in which they are found in the PATH directories, Cheers, Cedric Le 1/9/20 à 11:30, moibernabeu a écrit : > > Hi! > > I have two problems that prevent me using mcoffee: > > 1. > > TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE pid 57636 ppid > 56003. This error appears when I run the command > |$ t_coffee raw_sequences.fa -mode mcoffee| > How can I solve this to use mcoffee? > > 2. > > I usually install software in a concrete folder that is in PATH, > but, if I try to have alignment programs in this software folder > (downloaded from pages that appear at t_coffee introduction) > t_coffee does not recognize it. How can I redirect t_coffee to the > paths that are stored in .bash_profile (I'm in mac). > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <#34>, or unsubscribe > <https://github.com/notifications/unsubscribe-auth/ABML3KKTBVJJOKHMX7I7UZ3SDS5MRANCNFSM4QRP472A>. > -- ########################################## Dr Cedric Notredame, PhD Group Leader Notredame's lab - Comparative Bioinformatics Group Bioinformatics and Genomics Programme Room 440.03 Centre de Regulació Genòmica (CRG) Dr. Aiguader, 88 08003 Barcelona Spain Ph# + 34 93 316 02 71 Fax# + 34 93 316 00 99 Mobile# + 34 66 250 47 82 email ***@***.*** url www.tcoffee.org blog cedricnotredame.blogspot.com ORC-ID: 0000-0003-1461-0988 ########################################### — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#34 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AMQPMNB63V2RLGSIDCHCIW3SDS53VANCNFSM4QRP472A>.