On 27/08/2009 10.53, halford e. (eh506) wrote:
It seems that the problem with fneighbor depends above all on the number
of sequences used for the alignment!! and bootstraps
with 6 sequences you can use also 100 bootstraps and you obtain a
correct result instead with even 30 sequences and 2 bootstraps you got
error like this I suppose :
[Text: Soaplab call returned an error : Summary:
Completed: Erroneously
Termination status: 1
Started: 2009-Aug-27 13:54:32 (BST)
Ended: 2009-Aug-27 13:54:32 (BST)
Duration: 0:00:00.381
Report:
Some error messages were reported.
Name: phylogeny_distance_matrix.fneighbor
Job ID: [phylogeny_distance_matrix.fneighbor]_6e01e63d.123598c4c65.6168
Program and parameters:
/ebi/extserv/bin/EMBOSS-6.1.0/bin/fneighbor
-datafile
i_datafile
-treetype
n
-outfile
o_outfile
-outtreefile
o_outtreefiletreefile
-auto
--- end of parameters
Exit code: 1
Standard error stream:
Error: Distance file i_datafile
Error: Unable to read distances file 'i_datafile'
Died: fneighbor terminated: Bad value for '-datafile' with -auto defined
<br> SoaplabTask.execute(..) : line 146 <SoaplabTask.java><br>
ProcessorTask.runAndGenerateTemplates(..) : line 585
<ProcessorTask.java><br>
ProcessorTask.doInvocationWithRetryLogic(..) : line 524
<ProcessorTask.java><br> ProcessorTask.invokeOnce(..) : line 443
<ProcessorTask.java><br>
ProcessorTask.invokeWithoutIteration(..) : line 652
<ProcessorTask.java><br> ProcessorTask.invoke(..) : line 356
<ProcessorTask.java><br> ProcessorTask.handleRun(..) : line 282
<ProcessorTask.java><br> NewState$1.run(..) : line 67
<NewState.java><br>]
Strange behavior !!
I previously created a workflow which involves:
Edialign --> fprotdist --> fneighbour --> fdrawtree and fdrawgram
Much like in the workflow on myExperiment called 'Workflow for Protein Sequence
Analysis'.
This workflow works well.
However I am trying to incorporate in fseqboot and having read the
documentation have inserted it between Edialign and fprotdist. However the
workflow errors on fneighbour.
I connected 'outseq' of edialign to 'sequence_direct_data' of fseqboot and
'outfile' of fseq boot to 'sequence_direct_data' of fprotdist.
Does anyone know what I am doing wrong?
Thank you
Emily
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