Running vdjtools CalcBasicStats and PoolSamples fail on input file of 10xGenomics data from vdjdb

[ghost]

Describe the problem
I am aiming to run the .Rmd tutorial for the paper 'A Framework for Annotation of Antigen Specificities in High-Throughput T-Cell Repertoire Sequencing Studies' found here(https://github.com/antigenomics/tcr-annotation-methodology), by using the 10xGenomics data from vdjdb as input dataset. I have read the section 'Customizing the Framework for Analysis of User-Provided Datasets' of the paper to prepare my input dataset before using CalcBasicStats in the tutorial code. Currently I'm having errors when using the PoolSamples method of vdjtools to pre-process the 10x data.

To Reproduce
--Download 10xGenomics dataset from vdjdb:
-https://vdjdb.cdr3.net/search
-set parameters: species=human, gene(chain): TRB, paired only, Meta: search for 10xGenomics and select the only search result given
-refresh table
-export as .tsv with paired-gene-export enabled

--From a terminal (I used the Windows command prompt) run "java -jar {path_to_vdj_tools}/vdjtools-1.2.1.jar PoolSamples -i strict {path_to_data}/{10xData file}.tsv {output_prefix}"
No changes where made to the .tsv file after downloading it from vdjdb. Errors given by this execution are under the next header of this issue.
I have also tried with .txt (created using Python) and .txt.gz (created using 7zip) versions of the same file, but I still get the same errors.

--Clone the 'tcr-annotation-methodology ' repo from antigenomics, and in the tutorial.Rmd modify only this line with the input filename for 10xData:
run_java("vdjtools-1.2.1",
"CalcBasicStats data/control.txt.gz data/{INPUT_FILENAME_preprocessed from PoolSamples}.{extension} output/",
T)

Run the script up to and including the 'CalcBasicStats' line, using the pre-processed input file. Just out of curiosity, I tried to run it on the {10x_data_from_vdjdb}.tsv file (and the .txt and .txt.gz versions of the same file) as downloaded by vdjdb without any pre-processing, and I still get the same error as with PoolSamples.

Errors (with PoolSample)

C:\Users\Stelios\Documents\tcr-annotation-methodology-master>java -Xmx1G -jar C:/Users/Stelios/vdjsw/vdjtools-1.2.1.jar PoolSamples -i strict data/10x_vdjdb.tsv preprocessed_10x_vdjdb
Executing com.antigenomics.vdjtools.operate.PoolSamples -i strict data/10x_vdjdb.tsv preprocessed_10x_vdjdb
[Tue Dec 22 11:56:20 EET 2020 PoolSamples] Reading samples
[Tue Dec 22 11:56:20 EET 2020 PoolSamples] 1 samples loaded
[Tue Dec 22 11:56:20 EET 2020 PoolSamples] Pooling with Strict, this may take a while
[Tue Dec 22 11:56:20 EET 2020 SampleStreamConnection] Loading sample 10x_vdjdb
[ERROR] java.lang.RuntimeException: Unable to parse clonotype string 1 TRB CASSEGWHSYEQYF TRBV6-101 TRBJ2-701 HomoSapiens HLA-A03:01 B2M MHCI KLGGALQAK IE1 CMV https://www.10xgenomics.com/resources/application-notes/a-new-way-of-exploring-immunity-linking-highly-multiplexed-antigen-recognition-to-immune-repertoire-and-phenotype/# {"frequency": "1/11684", "identification": "dextramer-sort", "sequencing": "rna-seq", "singlecell": "yes", "verification": ""} {"cell.subset": "", "clone.id": "", "donor.MHC": "", "donor.MHC.method": "", "epitope.id": "", "replica.id": "", "samples.found": 1, "structure.id": "", "studies.found": 1, "study.id": "", "subject.cohort": "", "subject.id": "1", "tissue": ""} {"cdr3": "CASSEGWHSYEQYF", "cdr3_old": "CASSEGWHSYEQYF", "fixNeeded": false, "good": true, "jCanonical": true, "jFixType": "NoFixNeeded", "jId": "TRBJ2-701", "jStart": 8, "vCanonical": true, "vEnd": 5, "vFixType": "NoFixNeeded", "vId": "TRBV6-1*01"} 0 for VDJtools input type: For input string: "TRB", see _vdjtools_error.log for details

_vdjtools_error.log:
[Tue Dec 22 11:56:20 EET 2020 BEGIN]
[Script]
PoolSamples
[CommandLine]
executing vdjtools-1.2.1.jar PoolSamples -i strict data/10x_vdjdb.tsv preprocessed_10x_vdjdb
[Message]
java.lang.RuntimeException: Unable to parse clonotype string 1 TRB CASSEGWHSYEQYF TRBV6-101 TRBJ2-701 HomoSapiens HLA-A03:01 B2M MHCI KLGGALQAK IE1 CMV https://www.10xgenomics.com/resources/application-notes/a-new-way-of-exploring-immunity-linking-highly-multiplexed-antigen-recognition-to-immune-repertoire-and-phenotype/# {"frequency": "1/11684", "identification": "dextramer-sort", "sequencing": "rna-seq", "singlecell": "yes", "verification": ""} {"cell.subset": "", "clone.id": "", "donor.MHC": "", "donor.MHC.method": "", "epitope.id": "", "replica.id": "", "samples.found": 1, "structure.id": "", "studies.found": 1, "study.id": "", "subject.cohort": "", "subject.id": "1", "tissue": ""} {"cdr3": "CASSEGWHSYEQYF", "cdr3_old": "CASSEGWHSYEQYF", "fixNeeded": false, "good": true, "jCanonical": true, "jFixType": "NoFixNeeded", "jId": "TRBJ2-701", "jStart": 8, "vCanonical": true, "vEnd": 5, "vFixType": "NoFixNeeded", "vId": "TRBV6-101"} 0 for VDJtools input type: For input string: "TRB"
[StackTrace-Short]
com.antigenomics.vdjtools.io.parser.ClonotypeStreamParser.parse(ClonotypeStreamParser.groovy:189)
com.antigenomics.vdjtools.io.parser.ClonotypeStreamParser$_iterator_closure8.doCall(ClonotypeStreamParser.groovy:249)
com.antigenomics.vdjtools.io.parser.ClonotypeStreamParser$_iterator_closure8.doCall(ClonotypeStreamParser.groovy)
com.antigenomics.vdjtools.sample.Sample.fromInputStream(Sample.java:174)
com.antigenomics.vdjtools.sample.Sample$fromInputStream.call(Unknown Source)
com.antigenomics.vdjtools.io.SampleStreamConnection._load(SampleStreamConnection.groovy:128)
com.antigenomics.vdjtools.io.SampleStreamConnection.getSample(SampleStreamConnection.groovy:139)
com.antigenomics.vdjtools.sample.SampleCollection$_iterator_closure6.doCall(SampleCollection.groovy:320)
com.antigenomics.vdjtools.sample.SampleCollection$_iterator_closure6.doCall(SampleCollection.groovy)
com.antigenomics.vdjtools.pool.SampleAggregator.(SampleAggregator.java:81)
com.antigenomics.vdjtools.operate.PoolSamples.run(PoolSamples.groovy:119)
com.antigenomics.vdjtools.operate.PoolSamples$run.call(Unknown Source)
com.antigenomics.vdjtools.misc.ExecUtil.run(ExecUtil.groovy:94)
com.antigenomics.vdjtools.misc.ExecUtil$run.call(Unknown Source)
com.antigenomics.vdjtools.VdjTools.run(VdjTools.groovy:226)
com.antigenomics.vdjtools.VdjTools.main(VdjTools.groovy)
[StackTrace-Full]
java.lang.RuntimeException: Unable to parse clonotype string 1 TRB CASSEGWHSYEQYF TRBV6-101 TRBJ2-701 HomoSapiens HLA-A03:01 B2M MHCI KLGGALQAK IE1 CMV https://www.10xgenomics.com/resources/application-notes/a-new-way-of-exploring-immunity-linking-highly-multiplexed-antigen-recognition-to-immune-repertoire-and-phenotype/# {"frequency": "1/11684", "identification": "dextramer-sort", "sequencing": "rna-seq", "singlecell": "yes", "verification": ""} {"cell.subset": "", "clone.id": "", "donor.MHC": "", "donor.MHC.method": "", "epitope.id": "", "replica.id": "", "samples.found": 1, "structure.id": "", "studies.found": 1, "study.id": "", "subject.cohort": "", "subject.id": "1", "tissue": ""} {"cdr3": "CASSEGWHSYEQYF", "cdr3_old": "CASSEGWHSYEQYF", "fixNeeded": false, "good": true, "jCanonical": true, "jFixType": "NoFixNeeded", "jId": "TRBJ2-701", "jStart": 8, "vCanonical": true, "vEnd": 5, "vFixType": "NoFixNeeded", "vId": "TRBV6-101"} 0 for VDJtools input type: For input string: "TRB"
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
at java.lang.reflect.Constructor.newInstance(Unknown Source)
at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:83)
at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:77)
at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:59)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:238)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:258)
at com.antigenomics.vdjtools.io.parser.ClonotypeStreamParser.parse(ClonotypeStreamParser.groovy:189)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:104)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:326)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:352)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:68)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:157)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:169)
at com.antigenomics.vdjtools.io.parser.ClonotypeStreamParser$_iterator_closure8.doCall(ClonotypeStreamParser.groovy:249)
at com.antigenomics.vdjtools.io.parser.ClonotypeStreamParser$_iterator_closure8.doCall(ClonotypeStreamParser.groovy)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:104)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:326)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:264)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1041)
at groovy.lang.Closure.call(Closure.java:421)
at org.codehaus.groovy.runtime.ConvertedMap.invokeCustom(ConvertedMap.java:54)
at org.codehaus.groovy.runtime.ConversionHandler.invoke(ConversionHandler.java:124)
at com.sun.proxy.$Proxy4.next(Unknown Source)
at com.antigenomics.vdjtools.sample.Sample.fromInputStream(Sample.java:174)
at com.antigenomics.vdjtools.sample.Sample$fromInputStream.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
at com.antigenomics.vdjtools.io.SampleStreamConnection._load(SampleStreamConnection.groovy:128)
at com.antigenomics.vdjtools.io.SampleStreamConnection.getSample(SampleStreamConnection.groovy:139)
at com.antigenomics.vdjtools.sample.SampleCollection$_iterator_closure6.doCall(SampleCollection.groovy:320)
at com.antigenomics.vdjtools.sample.SampleCollection$_iterator_closure6.doCall(SampleCollection.groovy)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:104)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:326)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:264)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1041)
at groovy.lang.Closure.call(Closure.java:421)
at org.codehaus.groovy.runtime.ConvertedMap.invokeCustom(ConvertedMap.java:54)
at org.codehaus.groovy.runtime.ConversionHandler.invoke(ConversionHandler.java:124)
at com.sun.proxy.$Proxy4.next(Unknown Source)
at com.antigenomics.vdjtools.pool.SampleAggregator.(SampleAggregator.java:81)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
at java.lang.reflect.Constructor.newInstance(Unknown Source)
at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:83)
at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrapNoCoerce.callConstructor(ConstructorSite.java:105)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:59)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:238)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:266)
at com.antigenomics.vdjtools.operate.PoolSamples.run(PoolSamples.groovy:119)
at com.antigenomics.vdjtools.operate.PoolSamples$run.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:120)
at com.antigenomics.vdjtools.misc.ExecUtil.run(ExecUtil.groovy:94)
at com.antigenomics.vdjtools.misc.ExecUtil$run.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:136)
at com.antigenomics.vdjtools.VdjTools.run(VdjTools.groovy:226)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:104)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:326)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1235)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1041)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:1018)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:1001)
at org.codehaus.groovy.runtime.InvokerHelper.runScript(InvokerHelper.java:423)
at org.codehaus.groovy.runtime.InvokerHelper$runScript.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:136)
at com.antigenomics.vdjtools.VdjTools.main(VdjTools.groovy)
Caused by: java.lang.NumberFormatException: For input string: "TRB"
at sun.misc.FloatingDecimal.readJavaFormatString(Unknown Source)
at sun.misc.FloatingDecimal.parseDouble(Unknown Source)
at java.lang.Double.parseDouble(Unknown Source)
at java.lang.Double.valueOf(Unknown Source)
at org.codehaus.groovy.runtime.StringGroovyMethods.toDouble(StringGroovyMethods.java:3454)
at org.codehaus.groovy.runtime.dgm$1212.invoke(Unknown Source)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:246)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:55)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:120)
at com.antigenomics.vdjtools.io.parser.BaseParser.innerParse(BaseParser.groovy:65)
at com.antigenomics.vdjtools.io.parser.ClonotypeStreamParser.parse(ClonotypeStreamParser.groovy:159)
... 82 more
[END]

Expected behavior
PoolSamples should run with no errors and output a pre-processed version of the given dataset. Then after doing step 2, a basicstats.txt file and other from the CalcBasicStats routine are calculated for the control and samples of interest files, without any errors.

Additional context
OS: Windows 10
Java version:
java version "1.8.0_271"
Java(TM) SE Runtime Environment (build 1.8.0_271-b09)
Java HotSpot(TM) 64-Bit Server VM (build 25.271-b09, mixed mode)
R version: 4.0.3
Python version: 3.8.5