Post

2 followers Follow
0
Avatar

Plugin wrapper error

Hi,

I'm trying to get a plugin wrapper going. I've used a similar wrapper setup on another installation of Geneious and it worked will. When I try to run the current plugin I get the following error:

Cause: com.biomatters.geneious.publicapi.plugin.DocumentOperationException at com.biomatters.iseek.plugin.wrapperplugins.WrapperOperation.a(WrapperOperation.java:442) at com.biomatters.iseek.plugin.wrapperplugins.WrapperOperation.b(WrapperOperation.java:221) at com.biomatters.iseek.plugin.wrapperplugins.WrapperOperation.a(WrapperOperation.java:149) at com.biomatters.iseek.plugin.wrapperplugins.WrapperOperation.performOperation(WrapperOperation.java:125) at com.biomatters.geneious.publicapi.plugin.DocumentOperation.performOperation(DocumentOperation.java:464) at com.biomatters.geneious.publicapi.plugin.DocumentOperation.performOperation(DocumentOperation.java:410) at com.biomatters.iseek.plugin.V.run(OperationManager.java:595) at com.biomatters.geneious.common.operations.b.a(OperationsUtilities.java:138) at com.biomatters.geneious.common.operations.b.a(OperationsUtilities.java:135) at com.biomatters.geneious.common.operations.a$c.b(OperationsUtilities.java:114) at com.biomatters.geneious.common.operations.a$b.a(OperationsUtilities.java:135) at com.biomatters.iseek.plugin.f.a(OperationManager.java:592) at com.biomatters.iseek.plugin.f$a.a(OperationManager.java:346) at com.biomatters.iseek.plugin.OperationManager$3.performAction(OperationManager.java:274) at com.biomatters.iseek.plugin.OperationManager$3.access$500(OperationManager.java:196) at com.biomatters.iseek.plugin.M.run(OperationManager.java:234) at java.lang.Thread.run(Unknown Source)

 

There is no error from the plugin executable.

 

This takes as input a set of sequences as a fasta file, identifies replicates, and exports a fasta file with representative sequences. I've attached the plugin below. Is there anything obvious that I'm missing here?

 

Thanks for your help.

 

Chris




usearch prefix dereplication_1.0.gplugin
Christopher Garay

Please sign in to leave a comment.

9 comments

0
Avatar

Sorry for the late reply, that means the command line tool is returning a non-0 exit code. Does that help? You can try running the same command directly from the command line to see if anything is printed to standard error.

For 9.0.1 I've made it display the exit code as part of the error message that is displayed.

Richard Moir 0 votes
Comment actions Permalink
0
Avatar

Thanks, Richard. It works well on the command line with the following command:

usearch.exe -derep_prefix in.fa -fastaout output -sizeout

I've changed the Comand Line option for the plugin to the following:

-derep_prefix [inputFileNames] -fastaout output -sizeout

So these should work similarly. After a run on the command line %errorlevel% is 0 so it does yield the correct exit code when working correctly. Could the error be due to the Document Type? These sequences are in one list. I currently have "Unaligned Sequences (2+)" selected.

Chris

 

Christopher Garay 0 votes
Comment actions Permalink
0
Avatar

The plugin is actually working fine for me. Just to check its not the input data which is causing a problem can you run it on the "yghJ Ion Torrent reads" sequence list in the "Contig Assembly" folder of the sample documents? That one works for me and returns 2,464 sequences.

Richard Moir 0 votes
Comment actions Permalink
0
Avatar

I just tried this on "yghJ Ion Torrent reads" and I see the same "Operation failed" dialog.

Christopher Garay 0 votes
Comment actions Permalink
0
Avatar

I just downloaded the R9 beta. This is now working well for me.

Christopher Garay 0 votes
Comment actions Permalink
0
Avatar

That's odd, but I'm glad you got it working. let us know if you need any more help.

If you're doing dereplication you could also try out the Remove Duplicate Reads function under the Sequence menu in R9. It might be interesting to compare against.

Richard Moir 0 votes
Comment actions Permalink
0
Avatar

I am seeing this issue again with 9.0.2. I am using the same executable but using flag to run a different algorithm. There is a more informative error code this time: -1073741515 (or 0xC0000135).

Christopher Garay 0 votes
Comment actions Permalink
0
Avatar

I meant to give you the full text of the error:

 

"Operation failed. The error was:

Failed to run: C:\Users\cgaray\Geneious 9.0 Data\WrapperPluginDevelopment\usearch prefix derep\usearch.exe -derep_prefix input.fasta -fastaout output -sizeout, exit code: -1073741515

usearch prefix derep reported no error messages

Cause: Failed to run: C:\Users\cgaray\Geneious 9.0 Data\WrapperPluginDevelopment\usearch prefix derep\usearch.exe -derep_prefix input.fasta -fastaout output -sizeout, exit code: -1073741515 com.biomatters.geneious.publicapi.plugin.DocumentOperationException at com.biomatters.iseek.plugin.wrapperplugins.WrapperOperation.a(WrapperOperation.java:443) at com.biomatters.iseek.plugin.wrapperplugins.WrapperOperation.b(WrapperOperation.java:221) at com.biomatters.iseek.plugin.wrapperplugins.WrapperOperation.a(WrapperOperation.java:149) at com.biomatters.iseek.plugin.wrapperplugins.WrapperOperation.performOperation(WrapperOperation.java:125) at com.biomatters.geneious.publicapi.plugin.DocumentOperation.performOperation(DocumentOperation.java:464) at com.biomatters.geneious.publicapi.plugin.DocumentOperation.performOperation(DocumentOperation.java:410) at com.biomatters.iseek.plugin.operations.p.run(OperationManager.java:453) at com.biomatters.geneious.common.operations.b.a(OperationsUtilities.java:139) at com.biomatters.geneious.common.operations.b.a(OperationsUtilities.java:136) at com.biomatters.geneious.common.operations.a$c.b(OperationsUtilities.java:115) at com.biomatters.geneious.common.operations.a$b.a(OperationsUtilities.java:136) at com.biomatters.iseek.plugin.operations.e.a(OperationManager.java:447) at com.biomatters.iseek.plugin.operations.u.a(OperationPerformer.java:98) at com.biomatters.iseek.plugin.operations.OperationAction.performAction(OperationAction.java:121) at com.biomatters.iseek.plugin.operations.OperationAction.access$000(OperationAction.java:29) at com.biomatters.iseek.plugin.operations.a.run(OperationAction.java:84) at java.lang.Thread.run(Thread.java:745)"

 

 

 

Christopher Garay 0 votes
Comment actions Permalink