T-Coffee misinterpret an input file starting with a "A"

[pditommaso]

To replicate the issue:

$ t_coffee -infile ASA.fasta -in Mproba_pair -score 1

ERROR: SSA.fasta not recognised [FATAL:T-COFFEE]
INPUT FILES
    Input File (M) proba_pair 
    Input File (S) SA.fasta ERROR: SA.fasta Does Not Exist [FATAL:T-COFFEE]

Release: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477)

[cnotred]

The reason is some internal tagging being done by T-Coffee, with A for
Alignments and S for sequences. Normally, this should not interfere with
file names, but it not be well supported by the -infile flag.

The easiest fiy is to add the letter A before every filename provided
via -infile. If your file is name ASA.fasta, try:

t_coffee -infile AASA.fasta -in Mproba_pair -score 1

It is ugly but it works (it will work with any other file of course)

Cedric

On 1/4/15 1:54 PM, Paolo Di Tommaso wrote:

To replicate the issue:

|$ t_coffee -infile ASA.fasta -in Mproba_pair -score 1

ERROR: SSA.fasta not recognised [FATAL:T-COFFEE]
INPUT FILES
Input File (M) proba_pair
Input File (S) SA.fasta ERROR: SA.fasta Does Not Exist [FATAL:T-COFFEE]
|

Release: |T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision
8cbe486 - Build 477)|

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