antigenomics / vdjmatch Goto Github PK

Hello, the links to the VDJtools format readthedocs (in the README) section do not appear to be working. Please could you include an example sample in the repo as a reference in the meantime?

Facing uploading error

c.v.com - User [email protected]: Error while rendering sample SAM_121_clones

Hi,
Is there any way I can retain subjects and cells identifiers when converting TCR data into VDJdb annotation input format? I used the following command line-
java -jar vdjtools-1.2.1/vdjtools-1.2.1.jar Convert -S mixcr TCRA-TCRB_for-annotation.txt rrf_convert

I don't know if you have noticed http://friedmanlab.weizmann.ac.il/McPAS-TCR/ and they provide another TCR-Epitope.peptide database, which can be downloaded at http://friedmanlab.weizmann.ac.il/McPAS-TCR/session/96c097c9fefe5349ceec7cebd0308804/download/downloadDB?w=

I'm wondering if you can combine this database with vdjdb database that can have a larger database for the analysis.

• Don't report summary at all?
• Fix columns for reporting summary?
• Do via python/R?
• Create some database summary file for normalization

subj.

Use http://imperceptiblethoughts.com/shadow/ ?

When building using maven with Java 8, build fails with following error messages:

[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) on project vdjdb: Compilation failure: Compilation failure:
[ERROR] /Volumes/Data/Projects/MiLaboratory/vdjdb/src/main/groovy/com/antigenomics/vdjdb/core/db/CdrDatabase.groovy:[27,7] 1. ERROR in /Volumes/Data/Projects/MiLaboratory/vdjdb/src/main/groovy/com/antigenomics/vdjdb/core/db/CdrDatabase.groovy (at line 27)
[ERROR] class CdrDatabase implements Iterable<CdrEntrySet> {
[ERROR] ^^^^^^^^^^^
[ERROR] Groovy:Can't have an abstract method in a non-abstract class. The class 'com.antigenomics.vdjdb.core.db.CdrDatabase' must be declared abstract or the method 'void forEach(java.util.function.Consumer)' must be implemented.
[ERROR]
[ERROR] /Volumes/Data/Projects/MiLaboratory/vdjdb/src/main/groovy/com/antigenomics/vdjdb/core/db/CdrDatabase.groovy:[27,7] 2. ERROR in /Volumes/Data/Projects/MiLaboratory/vdjdb/src/main/groovy/com/antigenomics/vdjdb/core/db/CdrDatabase.groovy (at line 27)
[ERROR] class CdrDatabase implements Iterable<CdrEntrySet> {
[ERROR] ^^^^^^^^^^^
[ERROR] Groovy:Can't have an abstract method in a non-abstract class. The class 'com.antigenomics.vdjdb.core.db.CdrDatabase' must be declared abstract or the method 'java.util.Spliterator spliterator()' must be implemented.
[ERROR]
[ERROR] /Volumes/Data/Projects/MiLaboratory/vdjdb/src/main/groovy/com/antigenomics/vdjdb/core/db/CdrEntrySet.groovy:[6,7] 3. ERROR in /Volumes/Data/Projects/MiLaboratory/vdjdb/src/main/groovy/com/antigenomics/vdjdb/core/db/CdrEntrySet.groovy (at line 6)
[ERROR] class CdrEntrySet implements Iterable<CdrEntry> {
[ERROR] ^^^^^^^^^^^
[ERROR] Groovy:Can't have an abstract method in a non-abstract class. The class 'com.antigenomics.vdjdb.core.db.CdrEntrySet' must be declared abstract or the method 'void forEach(java.util.function.Consumer)' must be implemented.
[ERROR]
[ERROR] /Volumes/Data/Projects/MiLaboratory/vdjdb/src/main/groovy/com/antigenomics/vdjdb/core/db/CdrEntrySet.groovy:[6,7] 4. ERROR in /Volumes/Data/Projects/MiLaboratory/vdjdb/src/main/groovy/com/antigenomics/vdjdb/core/db/CdrEntrySet.groovy (at line 6)
[ERROR] class CdrEntrySet implements Iterable<CdrEntry> {
[ERROR] ^^^^^^^^^^^
[ERROR] Groovy:Can't have an abstract method in a non-abstract class. The class 'com.antigenomics.vdjdb.core.db.CdrEntrySet' must be declared abstract or the method 'java.util.Spliterator spliterator()' must be implemented.

I think the issue can be solved by upgrading groovy compiler (current seems to fail to understand Java 8 default methods in interfaces).

Subj.

• Number of unique CDR3AA in each category
• Entries that were not found

Hi there,
It can run without antigen species filter and the output file will contain all the specific CDR3 in one sample .But when i try to run java -jar -Xmx4G vdjdb-1.1.5.jar -S human -R TRB --use-fat-db --filter=__antigen.species__ = "CMV" bSI2.txt CMVbSI2
it report error that sample missing no matter the use the pool.aa.table.txt or single sample file.

Is there any thing wrong of the code i write.
Thank you

manager@bl8vbox[manager] java -jar -Xmx4G vdjdb-1.1.5.jar -S human -R TRB --use-fat-db --filter=__antigen.species__ = "CMV" bSI2.txt CMVbSI2

  | [Thu Jul 13 03:51:54 UTC 2017 Main] Loading database...
  | [Thu Jul 13 03:51:58 UTC 2017 Main] Loaded database.
  | columns: complex.id,gene,cdr3,v.segm,j.segm,species,mhc.a,mhc.b,mhc.class,antigen.epitope,antigen.gene,antigen.species,reference.id,method,meta,cdr3fix,vdjdb.score,web.method,web.method.seq,web.cdr3fix.nc,web.cdr3fix.unmp, rows: 7427
  | [Thu Jul 13 03:51:58 UTC 2017 Main] Filtering using antigen.species.
  | [Thu Jul 13 03:54:19 UTC 2017 Main] Done.
  | columns: complex.id,gene,cdr3,v.segm,j.segm,species,mhc.a,mhc.b,mhc.class,antigen.epitope,antigen.gene,antigen.species,reference.id,method,meta,cdr3fix,vdjdb.score,web.method,web.method.seq,web.cdr3fix.nc,web.cdr3fix.unmp, rows: 7427
  | [Thu Jul 13 03:54:19 UTC 2017 Main] Preparing clonotype database for homosapiens TRB.
  | [Thu Jul 13 03:54:20 UTC 2017 Main] Done.
  | columns: complex.id,gene,cdr3,v.segm,j.segm,species,mhc.a,mhc.b,mhc.class,antigen.epitope,antigen.gene,antigen.species,reference.id,method,meta,cdr3fix,vdjdb.score,web.method,web.method.seq,web.cdr3fix.nc,web.cdr3fix.unmp, rows: 4427
  | [Thu Jul 13 03:54:20 UTC 2017 Main] Reading sample(s)...
  | Exception in thread "main" java.io.FileNotFoundException: Missing sample file =
  | at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
  | at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
  | at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
  | at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
  | at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:77)
  | at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:71)
  | at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:81)
  | at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:57)
  | at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:182)
  | at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:190)
  | at com.antigenomics.vdjtools.sample.SampleCollection$_closure1.doCall(SampleCollection.groovy:156)
  | at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
  | at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
  | 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:90)
  | at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:233)
  | at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:272)
  | at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:909)
  | at groovy.lang.Closure.call(Closure.java:423)
  | at groovy.lang.Closure.call(Closure.java:439)
  | at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:1373)
  | at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:1366)
  | at org.codehaus.groovy.runtime.dgm$149.invoke(Unknown Source)
  | at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:271)
  | at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:53)
  | at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:45)
  | at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:108)
  | at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
  | at com.antigenomics.vdjtools.sample.SampleCollection.(SampleCollection.groovy:150)
  | at com.antigenomics.vdjtools.sample.SampleCollection.(SampleCollection.groovy)
  | at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
  | at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
  | at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
  | at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
  | at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:77)
  | at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrapNoCoerce.callConstructor(ConstructorSite.java:102)
  | at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:57)
  | at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:182)
  | at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:194)
  | at com.antigenomics.vdjdb.Main.run(Main.groovy:194)
  | at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
  | at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
  | at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  | at java.lang.reflect.Method.invoke(Method.java:498)
  | at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:90)
  | at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:233)
  | at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1085)
  | at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:909)
  | at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:901)
  | at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:884)
  | at org.codehaus.groovy.runtime.InvokerHelper.runScript(InvokerHelper.java:406)
  | at org.codehaus.groovy.runtime.InvokerHelper$runScript.call(Unknown Source)
  | at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:45)
  | at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:108)
  | at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:120)
  | at com.antigenomics.vdjdb.Main.main(Main.groovy)

Hi there,
I've built using Gradle, and it says 'BUILD SUCCESSFUL' - but when I try to run the program, I get
"Error: Unable to access jarfile vdjdb.jar" and indeed I'm unable to find the vdjdb.jar file.

Any chance you could help?
Many thanks,
Hugo

subj.

Put database to resources