Exporting IGMT gaped from custom reference

[pursellta]

I am using a custom reference that I built using mixcr and am trying to compare the allelic outputs with that of a different tool that requires a IGMT gapped alignment of the germline reference. I found the code to do this in the mixcr documentation but am unable to get it to work.

1. First I am using an external installation of repseqio; should I be using the built in one? If so how do I access it?
2. Second, when I run this code:
   repseqio fasta --imgt --species efuscus -g 'VRegion' ~/mixcr-4.6.0/libraries/efuscus-IG.json.gz ~/mixcr-4.6.0/libraries/vregion_gapped.fasta
   I get the following error:
   Exception in thread "main" java.lang.RuntimeException: com.fasterxml.jackson.databind.exc.UnrecognizedPropertyException: Unrecognized field "checksumVersion" (class io.repseq.dto.VDJCLibraryData), not marked as ignorable (5 known properties: "sequenceFragments", "speciesNames", "taxonId", "genes", "meta"]) at [Source: (BufferedInputStream); line: 6481, column: 24] (through reference chain: java.lang.Object[][0]->io.repseq.dto.VDJCLibraryData["checksumVersion"]) at com.milaboratory.o.bA.a(SourceFile:552) at com.milaboratory.o.bA.a(SourceFile:536) at com.milaboratory.o.bA.d(SourceFile:517) at io.repseq.cli.FastaAction.go(SourceFile:57) at io.repseq.cli.jcomander.JCommanderBasedMain.main(SourceFile:155) at io.repseq.cli.Main.main(SourceFile:91) Caused by: com.fasterxml.jackson.databind.exc.UnrecognizedPropertyException: Unrecognized field "checksumVersion" (class io.repseq.dto.VDJCLibraryData), not marked as ignorable (5 known properties: "sequenceFragments", "speciesNames", "taxonId", "genes", "meta"]) at [Source: (BufferedInputStream); line: 6481, column: 24] (through reference chain: java.lang.Object[][0]->io.repseq.dto.VDJCLibraryData["checksumVersion"]) at com.fasterxml.jackson.databind.exc.UnrecognizedPropertyException.from(UnrecognizedPropertyException.java:61) at com.fasterxml.jackson.databind.DeserializationContext.handleUnknownProperty(DeserializationContext.java:1132) at com.fasterxml.jackson.databind.deser.std.StdDeserializer.handleUnknownProperty(StdDeserializer.java:2202) at com.fasterxml.jackson.databind.deser.BeanDeserializerBase.handleUnknownProperty(BeanDeserializerBase.java:1705) at com.fasterxml.jackson.databind.deser.BeanDeserializerBase.handleUnknownVanilla(BeanDeserializerBase.java:1683) at com.fasterxml.jackson.databind.deser.BeanDeserializer.deserialize(BeanDeserializer.java:284) at com.fasterxml.jackson.databind.deser.BeanDeserializer._deserializeUsingPropertyBased(BeanDeserializer.java:463) at com.fasterxml.jackson.databind.deser.BeanDeserializerBase.deserializeFromObjectUsingNonDefault(BeanDeserializerBase.java:1405) at com.fasterxml.jackson.databind.deser.BeanDeserializer.deserializeFromObject(BeanDeserializer.java:352) at com.fasterxml.jackson.databind.deser.BeanDeserializer.deserialize(BeanDeserializer.java:185) at com.fasterxml.jackson.databind.deser.std.ObjectArrayDeserializer.deserialize(ObjectArrayDeserializer.java:216) at com.fasterxml.jackson.databind.deser.std.ObjectArrayDeserializer.deserialize(ObjectArrayDeserializer.java:26) at com.fasterxml.jackson.databind.deser.DefaultDeserializationContext.readRootValue(DefaultDeserializationContext.java:323) at com.fasterxml.jackson.databind.ObjectMapper._readMapAndClose(ObjectMapper.java:4730) at com.fasterxml.jackson.databind.ObjectMapper.readValue(ObjectMapper.java:3714) at com.milaboratory.o.bB.a(SourceFile:195) at com.milaboratory.o.bA.a(SourceFile:549) ... 5 more
   Any assistance would be much appreciated!

[mizraelson]

The issue seems to be with the repseqio version. Can you please reach out to us at support@milaboratories.com