Issues with legacy_blast.pl when using psicoffee mode

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fer...@gmail.com

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Sep 19, 2024, 1:08:29 PM9/19/24
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Hello group,

I have a transmembrane protein dataset, for which I want to use psicoffee for alignment. After browsing and digging around, I came up with the command:

t_coffee Pl-B2_s5_cdh70.fsa -mode psicoffee -blast_server LOCAL -protein_db /home/fer/Desktop/test/uniref90_TM/uniref90_TM.fasta

but I get:
INPUT FILES
Input File (M) proba_pair
Input File (S) Pl-B2_s5_cdh70.fsa  Format fasta_seq

Identify Master Sequences [no]:

Master Sequences Identified
Looking For Sequence Templates:

Template Type: [BLAST] Mode Or File: [BLAST] [Start
#*****************************************************************
--ERROR: #  [FATAL:T-COFFEE]

# The Program legacy_blast.pl Needed by T-COFFEE Could not be found
# If legacy_blast.pl is installed on your system:
#      -Make sure legacy_blast.pl is in your $path:
# If legacy_blast.pl is NOT installed obtain a copy from:
# ftp://ftp.ncbi.nih.gov/blast/executables/LATEST
#
#
# and install it manualy
******************************************************************


*************************************************************************************************
*                        FULL TRACE BACK PID: 46977                                    
46977 -- ERROR: #  [FATAL:T-COFFEE]
46977 -- COM: t_coffee Pl-B2_s5_cdh70.fsa -mode psicoffee -blast_server LOCAL -protein_db /home/fer/Desktop/test/uniref90_TM/uniref90_TM.fasta
46977 -- STACK: 46930 -> 46977
*************************************************************************************************

# TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE pid 46977 ppid 46930
#CL: t_coffee Pl-B2_s5_cdh70.fsa -mode psicoffee -blast_server LOCAL -protein_db /home/fer/Desktop/test/uniref90_TM/uniref90_TM.fasta

I have already manually installed the package containing legacy_blast.pl, which I have also added to $PATH (I checked and it's dicoverable). Also, the database was formatted with makeblastdb.
So, any ideas on what may be going on here? Thanks in advance! 
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