Missing value for option -score in clustalW

[guest]

When opening arb database.arb → menu sequence —→align sequence

---

select db file and press go gives error

+ LD_LIBRARY_PATH=/usr/lib/arb/lib:/usr/dt/lib:/usr/openwin/lib:/usr/lib/arb/lib/addlibs
+ export LD_LIBRARY_PATH
+ clustalw -output=PIR -infile=clus_in -align -quicktree -ktuple=1 -topdiags=5 -window=5 -pairgap=3 -score= -type=PROTEIN -transweight=0.5 -gapopen=10 -gapext=0.2 -maxdiv=30 -matrix=GONNET



 CLUSTAL 2.0.12 Multiple Sequence Alignments


Error: parameter required for -score
+ cat clus_in.pir
+ sed 's/^>DL;/#/g'
+ sed 's/^>P1;/%/g'
+ sed 's/^\*$//g'
cat: clus_in.pir: No such file or directory
+ arb_wait
Press return  to close window

The option is set but no value is assigned.

man clustalw

-score

PERCENT or ABSOLUTE.

option one: Remove the - score in the function that builds the command to use clustalW with this option,

That way only the default is possible and always used, ( i don't know what the default value is)

The cleaner and more flexible solution for all would be to add an dropdown in the form with the values PERCENT or ABSOLUTE. and the selected value/constant is used to set the value of the option of the clustalw command.

Labeled major, because the program doe snot run now, complaines about the missing parameter. when doing the same command manualy with PERCENT as value clustalW works ok.

[westram]

cropped

[westram]

arb 5.3 came with with CLUSTAL W (1.83). That combination works here.

Using another clustal version won't work.

[guest]

The server has a newer clustalw version for other tasks and programs.

If arb needs its own clustalW version it should prioritise the use of its own version with internal linking or by reference. so that 2 installs of clustalw can co exists. or implement the solution suggested whats the cleaner and more future proof solution.

kind regards what should this ticket be? feature request?

[westram]

Replying to guest:

If arb needs its own clustalW version it should prioritise the use of its own version with internal linking or by reference.

That's what arb originally does.

do you use some debian version of arb?

[epruesse]

Replying to guest:

what should this ticket be? feature request?

ARB 5 is "out of support". We simply don't have enough manpower to apply fixes to old versions. Could you upgrade to ARB 6 and check whether the issue persists? There are a lot of nice new things in ARB 6 that would speak for an upgrade anyway.