Hi,

I have alignments from Muscle in Fasta format, and i would like to obtain a consensus sequence using SeqLogo.

I saw that there is a component in Pipeline Pilot (v8) under Biology->Sequence Analysis->Readers->Utilities->Internals.

I give it a Fasta Alignment Reader component as input and a XY Scatter Plot Viewer as output.

However, i don't know how to configure the Sequence Logo component. It seems to be derivated from the bar chart component.

I tried to put accessionNumber as X Property and data as Y Property, but that throws me an error:

One or more properties of the required parameters is not defined or does not contain any values. For input string: "MMATITTSLFQRMGMMMKMMKFVLLFLLLLVLLFVSYAVSAEAVLSQAAEA"
java.lang.RuntimeException: One or more properties of the required parameters is not defined or does not contain any values. For input string: "MMATITTSLFQRMGMMMKMMKFVLLFLLLLVLLFVSYAVSAEAVLSQAAEA"
    at com.scitegic.report.component.chart.AbstractChartComponent.d(Unknown Source)
    at com.scitegic.report.component.AbstractAggregator.onProcess(Unknown Source)
    at com.scitegic.pilot.Pilot.callOnProcess(Pilot.java:300)
CComponentJavaPlugin::onProcess: Pipeline Pilot exception rethrown
-> Sequence Logo (Sequence Logo) - error during Data Record Processing phase
CProtocolStd::onProcess: Pipeline Pilot exception rethrown
CProtocol::onProcess: Pipeline Pilot exception rethrown
Protocol fetch_align_prune_logo, user qfab2: Pipeline Pilot exception caught
Protocol fetch_align_prune_logo, user qfab2: Protocol failed: Pipeline Pilot error
Pipeline Pilot Server version 8.0.1.500
Server OS: Linux puppis.qfab.org 2.6.18-92.1.17.el5 #1 SMP Wed Oct 22 04:19:38 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux

I didn't find neither documentation nor protocol that is using this component.

Any help would be appreciated.

Thank you.

Fred