Mirplex novel microrna identification error
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4.5 years ago

Hi, I am using mirplex to identify novel micrornas in plants. When I run it I get the following error. Can some one please help me solve this..

Jul 30, 2017 5:57:16 AM uk.ac.uea.cmp.srnaworkbench.utils.WorkbenchLogger log
SEVERE: WORKBENCH: NO_GENOME: Message: String index out of range: -6;
Stack Trace: java.lang.String.substring(Unknown Source)
uk.ac.uea.cmp.srnaworkbench.io.SRNAFastaReader.process(SRNAFastaReader.java:79)
uk.ac.uea.cmp.srnaworkbench.tools.mirplex.MirPlex.process(MirPlex.java:116)
uk.ac.uea.cmp.srnaworkbench.tools.RunnableTool.run(RunnableTool.java:329)
uk.ac.uea.cmp.srnaworkbench.tools.ToolBox$3.startTool(ToolBox.java:115)
uk.ac.uea.cmp.srnaworkbench.Main.startWorkbench(Main.java:218)
uk.ac.uea.cmp.srnaworkbench.Main.main(Main.java:43)

I am running it in windows.. The command I executed in command prompt

java -jar Workbench.jar --tool mirplex --params C:\Users\Vishweshwaran\Documents\data\parameters.cfg

On running the above command I get

**Parameters:
srna_file: C:\Users\Vishweshwaran\Documents\data\read_data.fastq
duplex_file: C:\Users\Vishweshwaran\Documents\data\xcx_output
build_duplexes: true
contig_analysis: true
contig_safe_abundance: 25
contig_kmer: 15
contig_min_length: 30
mature_filter_params: C:\Users\Vishweshwaran\Documents\data\mature_filter_params.txt
star_filter_params: C:\Users\Vishweshwaran\Documents\data\star_filter_params.txt
allowed_duplex_distance: -1
svm_model_file: C:\Users\Vishweshwaran\Documents\mirplex_v0.1\data\svm_models\plant_model1\out
svm_scaling_file: C:\Users\Vishweshwaran\Documents\mirplex_v0.1\data\svm_models\plant_model1
p_val_filter: 0.5
out_dir: C:\Users\Vishweshwaran\Documents\data\stevia_output\out
out_prefix: stevia
loci_validator: false
loci_known_mirnas:
loci_known_hairpins:
loci_genome:
loci_max_distance: 400**

Followed by this error..

Jul 30, 2017 6:24:58 AM uk.ac.uea.cmp.srnaworkbench.utils.WorkbenchLogger log
SEVERE: WORKBENCH: NO_GENOME: Message: String index out of range: -6;
Stack Trace: java.lang.String.substring(Unknown Source)
uk.ac.uea.cmp.srnaworkbench.io.SRNAFastaReader.process(SRNAFastaReader.java:79)
uk.ac.uea.cmp.srnaworkbench.tools.mirplex.MirPlex.process(MirPlex.java:116)
uk.ac.uea.cmp.srnaworkbench.tools.RunnableTool.run(RunnableTool.java:329)
uk.ac.uea.cmp.srnaworkbench.tools.ToolBox$3.startTool(ToolBox.java:115)
uk.ac.uea.cmp.srnaworkbench.Main.startWorkbench(Main.java:218)
uk.ac.uea.cmp.srnaworkbench.Main.main(Main.java:43)

Regards Vishwesh

next-gen mirplex • 1.1k views
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Entering edit mode

It's always helpful to specify how exactly you run this tool, such as which command you used and which steps were executed before this.

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Entering edit mode

Thanks.. I am running it in windows.. The command I executed in command prompt

java -jar Workbench.jar --tool mirplex --params C:\Users\Vishweshwaran\Documents\data\parameters.cfg

On running the above command I get

**Parameters:
srna_file: C:\Users\Vishweshwaran\Documents\data\read_data.fastq
duplex_file: C:\Users\Vishweshwaran\Documents\data\xcx_output
build_duplexes: true
contig_analysis: true
contig_safe_abundance: 25
contig_kmer: 15
contig_min_length: 30
mature_filter_params: C:\Users\Vishweshwaran\Documents\data\mature_filter_params.txt
star_filter_params: C:\Users\Vishweshwaran\Documents\data\star_filter_params.txt
allowed_duplex_distance: -1
svm_model_file: C:\Users\Vishweshwaran\Documents\mirplex_v0.1\data\svm_models\plant_model1\out
svm_scaling_file: C:\Users\Vishweshwaran\Documents\mirplex_v0.1\data\svm_models\plant_model1
p_val_filter: 0.5
out_dir: C:\Users\Vishweshwaran\Documents\data\stevia_output\out
out_prefix: stevia
loci_validator: false
loci_known_mirnas:
loci_known_hairpins:
loci_genome:
loci_max_distance: 400**

Followed by this error..

Jul 30, 2017 6:24:58 AM uk.ac.uea.cmp.srnaworkbench.utils.WorkbenchLogger log
SEVERE: WORKBENCH: NO_GENOME: Message: String index out of range: -6;
Stack Trace: java.lang.String.substring(Unknown Source)
uk.ac.uea.cmp.srnaworkbench.io.SRNAFastaReader.process(SRNAFastaReader.java:79)
uk.ac.uea.cmp.srnaworkbench.tools.mirplex.MirPlex.process(MirPlex.java:116)
uk.ac.uea.cmp.srnaworkbench.tools.RunnableTool.run(RunnableTool.java:329)
uk.ac.uea.cmp.srnaworkbench.tools.ToolBox$3.startTool(ToolBox.java:115)
uk.ac.uea.cmp.srnaworkbench.Main.startWorkbench(Main.java:218)
uk.ac.uea.cmp.srnaworkbench.Main.main(Main.java:43)

Regards Vishwesh

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Entering edit mode

I added (code) markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

101010 Button

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Their website describes some steps in debugging and searching for log files.

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Thanks...Yes The log files has the same error shown in the screen shots..

Jul 30, 2017 6:24:58 AM uk.ac.uea.cmp.srnaworkbench.utils.WorkbenchLogger log
SEVERE: WORKBENCH: NO_GENOME: Message: String index out of range: -6;
Stack Trace: java.lang.String.substring(Unknown Source)
uk.ac.uea.cmp.srnaworkbench.io.SRNAFastaReader.process(SRNAFastaReader.java:79)
uk.ac.uea.cmp.srnaworkbench.tools.mirplex.MirPlex.process(MirPlex.java:116)
uk.ac.uea.cmp.srnaworkbench.tools.RunnableTool.run(RunnableTool.java:329)
uk.ac.uea.cmp.srnaworkbench.tools.ToolBox$3.startTool(ToolBox.java:115)
uk.ac.uea.cmp.srnaworkbench.Main.startWorkbench(Main.java:218)
uk.ac.uea.cmp.srnaworkbench.Main.main(Main.java:43)
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0
Entering edit mode

In addition to what Wouter says, it helps to add the information to the question. That way, people don't have to read the comment threads to get the whole picture.

I've added the content from your comment to your question this time.

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Entering edit mode

Hello vishweshwaransridhar!

It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?p=209748#post209748

This is typically not recommended as it runs the risk of annoying people in both communities.

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