[EMBOSS] Bootstrap
Achille Zappa
achille.zappa at istge.it
Mon May 11 13:04:26 UTC 2009
> Hi Hamish,
>> EMBOSS 6.0.1 install updated with current patches.
> Thanks.
> Achille, I would appreciate it if you can update your workflow to Soaplab
> EMBOSS-6 services and check whether you now get correct results. Please
> let us know if you still get erroneous results.
> Regards,
> Mahmut
HI
I made some tests with EMBOSS-6 apps in Taverna 1.7.1, but i had bad
result, problably my faults because I haven't still exactly understand how
to use them.
I'll try to explain my doubts, sorry if it could be a little confused :
primarly my objective is to create phylogenetic trees of protein
sequences, so i use FASTA sequences for -> multiple alignments tolls to ->
create phylo trees with distance matrix (nj and/or UPGMA) or Maximum
Likelihood tools. For this I implemented in my workflow also a part like
that in the attach files :
- are the construction of the workflow, and connection links right?
- the fneighbor app fails everytime with errors like this :
"
Soaplab call returned an error : Summary:
Completed: Erroneously
Report:
Some error messages were reported.
Name: phylogeny_distance_matrix.fneighbor
Job ID: [phylogeny_distance_matrix.fneighbor]_583a12f0.1211f9ce9fb._79d0
Program and parameters:
/ebi/extserv/bin/EMBOSS-6.0.1/bin/fneighbor
-datafile
/ebi/extserv/soaplab-work/soaplab2_emboss6/SANDBOX
/[phylogeny_distance_matrix.fneighbor]_583a12f0.1211f9ce9fb._79d0/i_datafile
-outfile
/ebi/extserv/soaplab-work/soaplab2_emboss6/SANDBOX
/[phylogeny_distance_matrix.fneighbor]_583a12f0.1211f9ce9fb._79d0/o_outfile
-outtreefile
/ebi/extserv/soaplab-work/soaplab2_emboss6/SANDBOX
/[phylogeny_distance_matrix.fneighbor]_583a12f0.1211f9ce9fb._79d0
/o_outtreefiletreefile
-auto
--- end of parameters
Exit code: 1
Standard error stream:
Error: Distances file found 0 rows, expected 15
Error: Unable to read distances file '/ebi/extserv/soaplab-
work/soaplab2_emboss6/SANDBOX
/[phylogeny_distance_matrix.fneighbor]_583a12f0.1211f9ce9fb._79d0
/i_datafile'
Died: fneighbor terminated: Bad value for '-datafile' with -auto defined
<br> SoaplabTask.execute(..) : line 146 <SoaplabTask.java><br>
ProcessorTask.runAndGenerateTemplates(..) : line 576
<ProcessorTask.java><br>
ProcessorTask.doInvocationWithRetryLogic(..) : line 517
<ProcessorTask.java><br> ProcessorTask.invokeOnce(..) : line 436
<ProcessorTask.java><br> ProcessorTask.invokeWithoutIteration(..)
: line 642 <ProcessorTask.java><br> ProcessorTask.invoke(..) :
line 353 <ProcessorTask.java><br> ProcessorTask.handleRun(..) :
line 280 <ProcessorTask.java><br> NewState$1.run(..) : line 67
<NewState.java><br>]
"
I don't understand the "Standard error stream" explanation! about datafile
and the "-auto" param.
In attach also some input samples.
Instead If I use, for exsample, a 48 sequences alignment input I have a
java heap space error (is it my computer fault?).
-the timeout limit for the jobs is 60 minutes!? , it is a restriction of
EBI that is impossible to avoid I suppose!
for example a fproml job with 48 seq align is more than 60 minutes long I
think because after 1 hour it returns a completed job message with empty
output.
I apologize if all this stuff is only a my fault becuase of my ignorance
about these processes but I will appreciate your help and advices.
Thank you all for your time and disponibility
BEST REGARDS
CHEERS
Achille
P.S. Do you have some advices about the best tools for a phylogenetic tree
research, about different alignment apps (ClustalW, Muscle, T-coffee,
....) different distance algorythm (NJ, UPGMA, MAX Likelihood, ....), tree
constuction, computational optimization ...
THANKS
--
Achille Zappa
-Bioinformatics
National Cancer Research Institute (IST)
Largo Benzi 10
16132 Genova - ITALY
Tel. 010 5737288
-IEIIT - Sezione di Genova
National Research Council (CNR)
via De Marini, 6
16149 Genova - ITALY
Aiutaci TU ad aiutare TANTI: Il tuo 5 per MILLE a sostegno della nostra RICERCA.
Come fare:
Nella prossima dichiarazione dei redditi metti la firma
nell'apposito riquadro del 5 per mille,
scrivendo anche il codice fiscale dell'Istituto Nazionale per la Ricerca sul Cancro di Genova :
c.f. 80 100 850 108
Istituto Nazionale per la Ricerca sul Cancro
L.go R. Benzi, 10 -16132 Genova
http://www.istge.it
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