clustalw2, clustalw not running reliably from plugins with default install

[David Mathog]

t-coffee installed and clustalw2 is in plugins/linux. Yet this series
of commands:

module load t-coffee

set | grep COFF
CACHE_4_TCOFFEE=/tmp/TCOFFEE/cache

DIR_4_TCOFFEE=/usr/common/modules/el7/x86_64/software/t-coffee/13.39.0-CentOS-vanilla
LOCKDIR_4_TCOFFEE=/tmp/TCOFFEE/lockdir

PLUGINS_4_TCOFFEE=/usr/common/modules/el7/x86_64/software/t-coffee/13.39.0-CentOS-vanilla/plugins/linux

ROOT_T_COFFEE=/usr/common/modules/el7/x86_64/software/t-coffee/13.39.0-CentOS-vanilla
TMP_4_TCOFFEE=/tmp/TCOFFEE/tmp

t_coffee -method proba_pair -method lalign_id_pair -method
clustalw_pair \
-output score_ascii -output aln -output score_html -output
tcs_residue_filter3 \
-output tcs_column_filter3 -output tcs_residue_lower4 -output
tcs_weighted \
-output tcs_replicate_100 -outorder input -seqnos on \
-evaluate -infile input.aln

Logs these failures in the output file

--- Process Method/Library/Aln Mclustalw_pair
pid 7776 -- COMMAND FAILED: clustalw2
-INFILE=/tmp/TCOFFEE/tmp/tco/tcoqg2uisck7565//575797775519
-OUTFILE=/tmp/TCOFFEE/tmp/tco/tcoqg2uisck7565//575797775518
-OUTORDER=INPUT -NEWTREE=SCRATCH_FILE -align >>/dev/null 2>&1

We have another copy of clustalw2 available as a module and changing it
to

module load t-coffee
module load clustalw2

changes that section of the log file to:

--- Process Method/Library/Aln Mclustalw_pair
xxx Retrieved Mclustalw_pair

So there seems to be some issue of clustalw2 running from plugins.
Noticed that the default
protection set up by the install for

$PLUGINS_4_TCOFFEE/clustalw2

was not 755, and the run process was not the owner. Changed everything
in that directory
to 755 and, surprisingly, it made things worse! Then it ran with this
message:

#*****************************************************************
--ERROR: # [FATAL:T-COFFEE]

# The Program clustalw Needed by T-COFFEE Could not be found
# If clustalw is installed on your system:
# -Make sure clustalw is in your $path:
# If clustalw is NOT installed obtain a copy from:
# http://www.clustal.org
#
#
# and install it manualy


We also have a module for that and adding also:

module load clustalw

let everything run. So in summary, this works (starting from a clean
session each time):

module load t-coffee
module load clustalw2
module load clustalw
t-coffee (command as above)

as does this:

module load t-coffee
export PATH=$PLUGINS_4_TCOFFEE:$PATH
t-coffee (command as above)

but not this:

module load t-coffee
t-coffee (command as above)


Also, and this wasted a LOT of time, running the command overwrites the
input with
a slightly different version which exploded in -method lalign_id_pair,
apparently because
it sequence positions at the ends of the alignment lines added by
-seqnos on.

Regards,

David Mathog
mat...@caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech