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bzhanglab / neoflow

NeoFlow: a proteogenomics pipeline for neoantigen discovery
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Exception in thread "Task submitter" java.lang.NumberFormatException: For input string: "null" #4

Open EnHu359 opened 2 years ago

EnHu359 commented 2 years ago

I tried to use neoflow by exampledata.But I get an error when I run neoflow_msms.nf this is my code ./nextflow run ./neoflow-master/neoflow_msms.nf \ --ms /mnt/g/example_data/mgf \ --msms_para_file /mnt/g/example_data/comet_parameter.txt \ --search_engine comet --db ./test/customized_database/neoflow_crc_target_decoy.fasta --out_dir test2 \ --pv_refdb ./test/customized_database/ref.fasta --pv_tol 20 --pv_itol 0.05

then I get the following erros:

N E X T F L O W ~ version 21.10.6 Launching./neoflow-master/neoflow_msms.nf[reverent_watson] - revision: 9f41504eb3 Process multiple MS/MS files. [- ] process > msms_searching - [- ] process > calculate_fdr - [- ] process > prepare_pepquery_input - [- ] process > run_pepquery - [- ] process > add_pepquery_validation - WARN: Access to undefined parametercpu-- Initialise it to a default value eg.params.cpu = some_value` Error executing process > 'msms_searching (spec-00565.mgf)'

Caused by: For input string: "null"

Exception in thread "Task submitter" java.lang.NumberFormatException: For input string: "null" at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65) at java.lang.Integer.parseInt(Integer.java:580) at java.lang.Integer.valueOf(Integer.java:766) at org.codehaus.groovy.runtime.StringGroovyMethods.toInteger(StringGroovyMethods.java:3134) at org.codehaus.groovy.runtime.StringGroovyMethods.asType(StringGroovyMethods.java:192) at nextflow.extension.Bolts.asType(Bolts.groovy:449) at sun.reflect.GeneratedMethodAccessor12.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.codehaus.groovy.runtime.metaclass.ReflectionMetaMethod.invoke(ReflectionMetaMethod.java:54) at org.codehaus.groovy.runtime.metaclass.NewInstanceMetaMethod.invoke(NewInstanceMetaMethod.java:54) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1268) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035) at org.codehaus.groovy.runtime.InvokerHelper.invokePojoMethod(InvokerHelper.java:1017) at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:1008) at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethodN(ScriptBytecodeAdapter.java:180) at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.asType(ScriptBytecodeAdapter.java:603) at nextflow.processor.TaskConfig.getCpus(TaskConfig.groovy:282) at nextflow.processor.TaskConfig$getCpus$18.call(Unknown Source) at nextflow.processor.TaskHandler.getTraceRecord(TaskHandler.groovy:168) at nextflow.executor.LocalTaskHandler.super$2$getTraceRecord(LocalExecutor.groovy) at sun.reflect.GeneratedMethodAccessor336.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1268) at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethodOnSuperN(ScriptBytecodeAdapter.java:144) at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethodOnSuper0(ScriptBytecodeAdapter.java:164) at nextflow.executor.LocalTaskHandler.getTraceRecord(LocalExecutor.groovy:256) at nextflow.Session.notifyTaskComplete(Session.groovy:972) at nextflow.processor.TaskPollingMonitor.submitPendingTasks(TaskPollingMonitor.groovy:566) at nextflow.processor.TaskPollingMonitor.submitLoop(TaskPollingMonitor.groovy:387) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [- ] process > msms_searching - [- ] process > calculate_fdr - [- ] process > prepare_pepquery_input - [- ] process > run_pepquery - [- ] process > add_pepquery_validation - WARN: Access to undefined parameter cpu -- Initialise it to a default value eg. params.cpu = some_value Error executing process > 'msms_searching (spec-00565.mgf)'

Caused by: For input string: "null" ` Is there some one can help me? thank you very much!

WLYYYYY commented 1 year ago

Hello @wenbostar, sorry to tag you directly, but I got the same error almost one year after this issue was created:

neoflow_error_module_2

It would be very much appreaciated if you could provide some comment!

Sawakotx commented 1 year ago

Hello @wenbostar, sorry to tag you directly, but I got the same error almost one year after this issue was created: neoflow_error_module_2

It would be very much appreaciated if you could provide some comment!

Hello~ @WLYYYYY, I successed this step this morning. I add a line 'params.cpu = 0 ' in the neoflow_msms.nf, which looks like the code I show in the image below. image

Wish this solution will help you!