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<DIV><FONT face=Arial color=#000000 size=2>Hi,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>I'm new to Swift programming. I was able to run a swift script before, but I couldn't run it now. I'm wondering if someone can help me figure out why. The swift script, sites.xml, tc.data, and all the error messages are copied in this email. Thank you!</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Regards,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Chen, Yue</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>*********************</FONT></DIV>
<DIV><FONT face=Arial size=2>Swift script</FONT></DIV>
<DIV><FONT face=Arial size=2>*********************</FONT></DIV>
<DIV><FONT face=Arial size=2>type Fasta {}<BR>type PTMapOut {}<BR>type Solution {}<BR>type Inputfile {}</FONT></DIV>
<DIV><FONT face=Arial size=2>app (PTMapOut ofile) PTMap (Solution sfile, Fasta fastafile, Inputfile input, Inputfile parameter)<BR>{<BR> PTMap @filename(sfile) @filename(fastafile) @filename(input) @filename(parameter) </FONT><A href="mailto:stdout=@filename(ofile"><FONT face=Arial size=2>stdout=@filename(ofile</FONT></A><FONT face=Arial size=2>);<BR>}</FONT></DIV>
<DIV><FONT face=Arial size=2>Fasta texts[] <filesys_mapper;prefix="fasta">;</FONT></DIV>
<DIV><BR><FONT face=Arial size=2>doall(Fasta texts[])<BR>{<BR> Solution sfile <"BSASolution.mzXML">;<BR> Inputfile input <"inputs.txt">;<BR> Inputfile parameter <"parameters.txt">;<BR> foreach p in texts {<BR> PTMapOut r <regexp_mapper;<BR> </FONT><A href="mailto:source=@p"><FONT face=Arial size=2>source=@p</FONT></A><FONT face=Arial size=2>,<BR> match="fasta(.*)",<BR> transform="</FONT><A href="file://\\1.out"><FONT face=Arial size=2>\\1.out</FONT></A><FONT face=Arial size=2>"<BR> >;</FONT></DIV>
<DIV><FONT face=Arial size=2> r = PTMap(sfile, p, input, parameter);<BR> }<BR>}</FONT></DIV>
<DIV><FONT face=Arial size=2>// Main<BR>doall(texts);<BR></FONT></DIV>
<DIV><FONT face=Arial size=2>**************</FONT></DIV>
<DIV><FONT face=Arial size=2>sites.xml</FONT></DIV>
<DIV><FONT face=Arial size=2>**************</FONT></DIV>
<DIV><FONT face=Arial size=2><pool handle="localhost"><BR> <gridftp url="local://localhost" /><BR> <execution provider="local" /><BR> <workdirectory >/var/tmp</workdirectory><BR> <profile namespace="karajan" key="jobThrottle">0</profile><BR></pool><BR></FONT></DIV>
<DIV><FONT face=Arial size=2>**************</FONT></DIV>
<DIV><FONT face=Arial size=2>tc.data</FONT></DIV>
<DIV><FONT face=Arial size=2>**************</FONT></DIV>
<DIV><FONT face=Arial size=2>localhost echo /bin/echo INSTALLED INTEL32::LINUX null<BR>localhost cat /bin/cat INSTALLED INTEL32::LINUX null<BR>localhost ls /bin/ls INSTALLED INTEL32::LINUX null<BR>localhost grep /bin/grep INSTALLED INTEL32::LINUX null<BR>localhost sort /bin/sort INSTALLED INTEL32::LINUX null<BR>localhost paste /bin/paste INSTALLED INTEL32::LINUX null<BR>localhost PTMap /home/yuechen/PTMap/PTMap INSTALLED INTEL32::LINUX null<BR></FONT></DIV>
<DIV><FONT face=Arial size=2>**************</FONT></DIV>
<DIV><FONT face=Arial size=2>Error messages</FONT></DIV>
<DIV><FONT face=Arial size=2>**************</DIV></FONT>
<DIV><FONT face=Arial size=2>[yuechen@communicado PTMap]$ swift PTMap.swift<BR>Execution failed:<BR> java.lang.NullPointerException<BR> at org.globus.cog.abstraction.impl.common.task.ServiceImpl.toString(ServiceImpl.java:156)<BR> at java.lang.String.valueOf(String.java:2577)<BR> at java.lang.StringBuffer.append(StringBuffer.java:220)<BR> at org.globus.cog.karajan.workflow.nodes.grid.GridNode.function(GridNode.java:31)<BR> at org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.post(AbstractFunction.java:45)<BR> at org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.childCompleted(AbstractSequentialWithArguments.java:192)<BR> at org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:33)<BR> at org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:335)<BR> at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)<BR> at org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)<BR> at org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:173)<BR> at org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:299)<BR> at org.globus.cog.karajan.workflow.nodes.ExecuteFile.notificationEvent(ExecuteFile.java:163)<BR> at org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:335)<BR> at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)<BR> at org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)<BR> at org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:173)<BR> at org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:299)<BR> at org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)<BR> at org.globus.cog.karajan.workflow.nodes.Sequential.startNext(Sequential.java:51)<BR> at org.globus.cog.karajan.workflow.nodes.Sequential.childCompleted(Sequential.java:45)<BR> at org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:33)<BR> at org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:335)<BR> at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)<BR> at org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)<BR> at org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:173)<BR> at org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:299)<BR> at org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)<BR> at org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.childCompleted(AbstractSequentialWithArguments.java:192)<BR> at org.globus.cog.karajan.workflow.nodes.user.UserDefinedElement.childCompleted(UserDefinedElement.java:283)<BR> at org.globus.cog.karajan.workflow.nodes.user.SequentialImplicitExecutionUDE.childCompleted(SequentialImplicitExecutionUDE.java:85)<BR> at org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:33)<BR> at org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:335)<BR> at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)<BR> at org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)<BR> at org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:173)<BR> at org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:299)<BR> at org.globus.cog.karajan.workflow.nodes.If.childCompleted(If.java:30)<BR> at org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:33)<BR> at org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:335)<BR> at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)<BR> at org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)<BR> at org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:173)<BR> at org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:299)<BR> at org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)<BR> at org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.post(AbstractFunction.java:46)<BR> at org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.childCompleted(AbstractSequentialWithArguments.java:192)<BR> at org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:33)<BR> at org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:335)<BR> at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)<BR> at org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)<BR> at org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:173)<BR> at org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:299)<BR> at org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)<BR> at org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.post(AbstractFunction.java:46)<BR> at org.globus.cog.karajan.workflow.nodes.Sequential.startNext(Sequential.java:51)<BR> at org.globus.cog.karajan.workflow.nodes.Sequential.executeChildren(Sequential.java:27)<BR> at org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.executeChildren(AbstractFunction.java:40)<BR> at org.globus.cog.karajan.workflow.nodes.FlowContainer.execute(FlowContainer.java:63)<BR> at org.globus.cog.karajan.workflow.nodes.FlowNode.restart(FlowNode.java:240)<BR> at org.globus.cog.karajan.workflow.nodes.FlowNode.start(FlowNode.java:281)<BR> at org.globus.cog.karajan.workflow.nodes.FlowNode.controlEvent(FlowNode.java:393)<BR> at org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:332)<BR> at org.globus.cog.karajan.workflow.FlowElementWrapper.event(FlowElementWrapper.java:227)<BR> at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)<BR> at org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)<BR> at org.globus.cog.karajan.workflow.events.EventWorker.run(EventWorker.java:69)<BR></DIV></FONT>
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