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opencb / opencga

An Open Computational Genomics Analysis platform for big data genomics analysis. OpenCGA is maintained and develop by its parent company Zetta Genomics. Please contact support@zettagenomics.com for bug report and feature requests.
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Error annotating variants with Cellbase #233

Closed simonjwhite closed 9 years ago

simonjwhite commented 9 years ago

I am getting this error when annotating variants using the CellBase REST with the command line: ./opencga.sh studies annotate-variants

[pool-1-thread-7] ERROR org.opencb.cellbase.core.client.CellBaseClient - Error parsing response to : http://bioinfodev.hpc.cam.ac.uk/cellbase/webservices/rest/v3/hsapiens/genomic/variant/full_annotation?of=json [pool-1-thread-7] WARN org.opencb.opencga.storage.core.variant.annotation.CellBaseVariantAnnotator - CellBase REST fail. Error parsing http://bioinfodev.hpc.cam.ac.uk/cellbase/webservices/rest/v3/hsapiens/genomic/variant/full_annotation?of=json com.fasterxml.jackson.databind.JsonMappingException: Can not deserialize instance of java.util.LinkedHashMap out of START_ARRAY token at [Source: {"apiVersion":"v3","warning":"","error":"","queryOptions":{"metadata":true,"exclude":null,"include":null,"limit":1000,"skip":-1,"count":false,"of":"json"},"response":[{"id":"2:24246175:C:T","time":0,"dbTime":8,"numResults":1,"numTotalResults":1,"warningMsg":"","errorMsg":"","resultType":"","result":[{"chromosome":"2","start":24246175,"end":24246175,"reference":"C","alternate":"T","id":"rs12989842","consequenceTypes":[{"geneName":"MFSD2B","ensemblGeneId":"ENSG00000205639","ensemblTranscriptId":"ENST00000406420","strand":"+","biotype":"protein_coding","sequenceOntologyTerms":[{"accession":"SO:0001627","name":"intron_variant"}]},{"geneName":"MFSD2B","ensemblGeneId":"ENSG00000205639","ensemblTranscriptId":"ENST00000338315","strand":"+","biotype":"protein_coding","sequenceOntologyTerms":[{"accession":"SO:0001627","name":"intron_variant"}]},{"geneName":"MFSD2B","ensemblGeneId":"ENSG00000205639","ensemblTranscriptId":"ENST00000495018","strand":"+","biotype":"retained_intron","sequenceOntologyTerms":[{"accession":"SO:0001632","name":"downstream_gene_variant"}]},{"geneName":"MFSD2B","ensemblGeneId":"ENSG00000205639","ensemblTranscriptId":"ENST00000469562","strand":"+","biotype":"retained_intron","cdnaPosition":671,"sequenceOntologyTerms":[{"accession":"SO:0001792","name":"non_coding_transcript_exon_variant"},{"accession":"SO:0001619","name":"non_coding_transcript_variant"}]},{"geneName":"MFSD2B","ensemblGeneId":"ENSG00000205639","ensemblTranscriptId":"ENST00000453731","strand":"+","biotype":"nonsense_mediated_decay","sequenceOntologyTerms":[{"accession":"SO:0001631","name":"2KB_upstream_gene_variant"}]},{"sequenceOntologyTerms":[{"accession":"SO:0001566","name":"regulatory_region_variant"}]}],"conservation":[{"score":0.10100000351667404,"source":"phastCons"},{"score":0.5609999895095825,"source":"phylop"}],"expression":[{"experimentalFactor":"organism_part","factorValue":"muscle","experimentId":"E-MTAB-37","technologyPlatform":"A-AFFY-44","expression":"UP","pvalue":0.040676575},{"experimentalFactor":"organism_part","factorValue":"lung","experimentId":"E-MTAB-37","technologyPlatform":"A-AFFY-44","expression":"DOWN","pvalue":0.0024026963},{"experimentalFactor":"organism_part","factorValue":"pancreas","experimentId":"E-MTAB-37","technologyPlatform":"A-AFFY-44","expression":"UP","pvalue":0.0028612816},{"experimentalFactor":"organism_part","factorValue":"rectum","experimentId":"E-MTAB-37","technologyPlatform":"A-AFFY-44","expression":"DOWN","pvalue":0.012689069},{"experimentalFactor":"organism_part","factorValue":"colon","experimentId":"E-MTAB-37","technologyPlatform":"A-AFFY-44","expression":"DOWN","pvalue":8.967102E-8},{"experimentalFactor":"organism_part","factorValue":"mammary gland","experimentId":"E-MTAB-37","technologyPlatform":"A-AFFY-44","expression":"DOWN","pvalue":2.7247513E-13},{"experimentalFactor":"organism_part","factorValue":"central nervous system","experimentId":"E-MTAB-37","technologyPlatform":"A-AFFY-44","expression":"UP","pvalue":0.007743001},{"experimentalFactor":"organism_part","factorValue":"esophagus","experimentId":"E-MTAB-37","technologyPlatform":"A-AFFY-44","expression":"DOWN","pvalue":5.530729E-5},{"experimentalFactor":"organism_part","factorValue":"liver","experimentId":"E-MTAB-37","technologyPlatform":"A-AFFY-44","expression":"UP","pvalue":1.9055133E-6},{"experimentalFactor":"organism_part","factorValue":"placenta","experimentId":"E-GEOD-6573","technologyPlatform":"A-AFFY-44","expression":"DOWN","pvalue":3.1232613E-4},{"experimentalFactor":"organism_part","factorValue":"abdominal fat","experimentId":"E-GEOD-6573","technologyPlatform":"A-AFFY-44","expression":"DOWN","pvalue":7.5942015E-5},{"experimentalFactor":"organism_part","factorValue":"decidua","experimentId":"E-GEOD-6573","technologyPlatform":"A-AFFY-44","expression":"UP","pvalue":1.0490527E-5},{"experimentalFactor":"cell_type","factorValue":"PBMCs","experimentId":"E-GEOD-20677","technologyPlatform":"A-AFFY-44","expression":"DOWN","pvalue":2.0543034E-10},{"experimentalFactor":"organism_part","factorValue":"duodenum","experimentId":"E-GEOD-1862","technologyPlatform":"A-AFFY-9","expression":"UP","pvalue":0.013395938},{"experimentalFactor":"groups_369","factorValue":"brain","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.0},{"experimentalFactor":"organism_part","factorValue":"muscle","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":6.658688E-4},{"experimentalFactor":"groups_369","factorValue":"prostate 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ganglion","experimentId":"E-MTAB-24","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.01344419},{"experimentalFactor":"organism_part","factorValue":"heart","experimentId":"E-MTAB-24","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.029699326},{"experimentalFactor":"organism_part","factorValue":"trigeminal ganglion","experimentId":"E-MTAB-25","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.0060444074},{"experimentalFactor":"organism_part","factorValue":"placenta","experimentId":"E-MTAB-25","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":0.04156806},{"experimentalFactor":"organism_part","factorValue":"blood","experimentId":"E-MTAB-25","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":0.029589444},{"experimentalFactor":"organism_part","factorValue":"brain","experimentId":"E-MTAB-25","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":5.472256E-7},{"experimentalFactor":"organism_part","factorValue":"heart","experimentId":"E-MTAB-25","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.010433709},{"experimentalFactor":"organism_part","factorValue":"testis","experimentId":"E-TABM-130","technologyPlatform":"A-AFFY-44","expression":"DOWN","pvalue":0.0017508462},{"experimentalFactor":"organism_part","factorValue":"seminiferous tubule","experimentId":"E-TABM-130","technologyPlatform":"A-AFFY-44","expression":"DOWN","pvalue":0.011346296},{"experimentalFactor":"organism_part","factorValue":"muscle","experimentId":"E-TABM-130","technologyPlatform":"A-AFFY-44","expression":"UP","pvalue":0.008170757},{"experimentalFactor":"organism_part","factorValue":"cartilage","experimentId":"E-TABM-130","technologyPlatform":"A-AFFY-44","expression":"UP","pvalue":0.0133242095}],"geneDrugInteraction":[]}]}]}; line: 1, column: 25283](through reference chain: org.opencb.datastore.core.QueryResponse["response"]->java.util.ArrayList[0]->org.opencb.datastore.core.QueryResult["result"]->java.util.ArrayList[0]->org.opencb.biodata.models.variant.annotation.VariantAnnotation["geneDrugInteraction"]) at com.fasterxml.jackson.databind.JsonMappingException.from(JsonMappingException.java:148) at com.fasterxml.jackson.databind.DeserializationContext.mappingException(DeserializationContext.java:835) at com.fasterxml.jackson.databind.DeserializationContext.mappingException(DeserializationContext.java:831) at com.fasterxml.jackson.databind.deser.std.StdDeserializer._deserializeFromEmpty(StdDeserializer.java:839) at com.fasterxml.jackson.databind.deser.std.MapDeserializer.deserialize(MapDeserializer.java:338) at com.fasterxml.jackson.databind.deser.std.MapDeserializer.deserialize(MapDeserializer.java:26) at com.fasterxml.jackson.databind.deser.SettableBeanProperty.deserialize(SettableBeanProperty.java:523) at com.fasterxml.jackson.databind.deser.impl.MethodProperty.deserializeAndSet(MethodProperty.java:95) at com.fasterxml.jackson.databind.deser.impl.BeanPropertyMap.findDeserializeAndSet(BeanPropertyMap.java:285) at com.fasterxml.jackson.databind.deser.BeanDeserializer.vanillaDeserialize(BeanDeserializer.java:248) at com.fasterxml.jackson.databind.deser.BeanDeserializer.deserialize(BeanDeserializer.java:136) at com.fasterxml.jackson.databind.deser.std.CollectionDeserializer.deserialize(CollectionDeserializer.java:245) at com.fasterxml.jackson.databind.deser.std.CollectionDeserializer.deserialize(CollectionDeserializer.java:217) at com.fasterxml.jackson.databind.deser.std.CollectionDeserializer.deserialize(CollectionDeserializer.java:25) at com.fasterxml.jackson.databind.deser.SettableBeanProperty.deserialize(SettableBeanProperty.java:523) at com.fasterxml.jackson.databind.deser.impl.MethodProperty.deserializeAndSet(MethodProperty.java:95) at com.fasterxml.jackson.databind.deser.impl.BeanPropertyMap.findDeserializeAndSet(BeanPropertyMap.java:285) at com.fasterxml.jackson.databind.deser.BeanDeserializer.vanillaDeserialize(BeanDeserializer.java:248) at com.fasterxml.jackson.databind.deser.BeanDeserializer.deserialize(BeanDeserializer.java:136) at com.fasterxml.jackson.databind.deser.std.CollectionDeserializer.deserialize(CollectionDeserializer.java:245) at com.fasterxml.jackson.databind.deser.std.CollectionDeserializer.deserialize(CollectionDeserializer.java:217) at com.fasterxml.jackson.databind.deser.std.CollectionDeserializer.deserialize(CollectionDeserializer.java:25) at com.fasterxml.jackson.databind.deser.SettableBeanProperty.deserialize(SettableBeanProperty.java:523) at com.fasterxml.jackson.databind.deser.impl.MethodProperty.deserializeAndSet(MethodProperty.java:95) at com.fasterxml.jackson.databind.deser.impl.BeanPropertyMap.findDeserializeAndSet(BeanPropertyMap.java:285) at com.fasterxml.jackson.databind.deser.BeanDeserializer.vanillaDeserialize(BeanDeserializer.java:248) at com.fasterxml.jackson.databind.deser.BeanDeserializer.deserialize(BeanDeserializer.java:136) at com.fasterxml.jackson.databind.ObjectReader._bindAndClose(ObjectReader.java:1443) at com.fasterxml.jackson.databind.ObjectReader.readValue(ObjectReader.java:1081) at org.opencb.cellbase.core.client.CellBaseClient.restGetter(CellBaseClient.java:469) at org.opencb.cellbase.core.client.CellBaseClient.get(CellBaseClient.java:437) at org.opencb.cellbase.core.client.CellBaseClient.get(CellBaseClient.java:409) at org.opencb.cellbase.core.client.CellBaseClient.get(CellBaseClient.java:262) at org.opencb.opencga.storage.core.variant.annotation.CellBaseVariantAnnotator.getVariantAnnotationsREST(CellBaseVariantAnnotator.java:305) at org.opencb.opencga.storage.core.variant.annotation.CellBaseVariantAnnotator.getVariantAnnotationsREST(CellBaseVariantAnnotator.java:338) at org.opencb.opencga.storage.core.variant.annotation.CellBaseVariantAnnotator.getVariantAnnotationsREST(CellBaseVariantAnnotator.java:342) at org.opencb.opencga.storage.core.variant.annotation.CellBaseVariantAnnotator.getVariantAnnotationsREST(CellBaseVariantAnnotator.java:338) at org.opencb.opencga.storage.core.variant.annotation.CellBaseVariantAnnotator.getVariantAnnotationsREST(CellBaseVariantAnnotator.java:338) at org.opencb.opencga.storage.core.variant.annotation.CellBaseVariantAnnotator.getVariantAnnotationsREST(CellBaseVariantAnnotator.java:342) at org.opencb.opencga.storage.core.variant.annotation.CellBaseVariantAnnotator.getVariantAnnotationsREST(CellBaseVariantAnnotator.java:338) at org.opencb.opencga.storage.core.variant.annotation.CellBaseVariantAnnotator.getVariantAnnotationsREST(CellBaseVariantAnnotator.java:338) at org.opencb.opencga.storage.core.variant.annotation.CellBaseVariantAnnotator.getVariantAnnotationsREST(CellBaseVariantAnnotator.java:338) at org.opencb.opencga.storage.core.variant.annotation.CellBaseVariantAnnotator.lambda$createAnnotation$1(CellBaseVariantAnnotator.java:255) at org.opencb.commons.run.ParallelTaskRunner$TaskRunnable.run(ParallelTaskRunner.java:359) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) [pool-1-thread-7] ERROR org.opencb.opencga.storage.core.variant.annotation.CellBaseVariantAnnotator - CellBase REST error. Skipping variant. 2:24246175:C:T

j-coll commented 9 years ago

Hi Simon, It seems to be a problem with the version of the VariantAnnotation model. In the server bioinfodev.hpc.cam.ac.uk we have installed the lastest develop version of cellbase. You can access to the lastest release version in bioinfo.hpc.cam.ac.uk where models are slightly different.

Which version of OpenCGA are you using? Is this error happening with all variants, or only with a few of them?

simonjwhite commented 9 years ago

Hi Jacobo, I am using the master branch of opencga. As far as I can tell it is all the variants that this happening with, but I will check. I guess I will update the config to point at bioinfo rather than bioinfodev and see if that solves the problem.

Thanks, Simon

On Wed, Nov 4, 2015 at 4:15 AM, Jacobo Coll Moragón < notifications@github.com> wrote:

Hi Simon, It seems to be a problem with the version of the VariantAnnotation model. In the server bioinfodev.hpc.cam.ac.uk http://bioinfodev.hpc.cam.ac.uk/cellbase/webservices/rest/v3/hsapiens/genomic/variant/2:24246175:C:T/full_annotation?of=json we have installed the lastest develop version of cellbase. You can access to the lastest release version in bioinfo.hpc.cam.ac.uk http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/v3/hsapiens/genomic/variant/2:24246175:C:T/full_annotation?of=json where models are slightly different.

Which version of OpenCGA are you using? Is this error happening with all variants, or only with a few of them?

— Reply to this email directly or view it on GitHub https://github.com/opencb/opencga/issues/233#issuecomment-153671197.

simonjwhite commented 9 years ago

Yeah that seems to have worked, the "bioinfodev" URL is hard-coded in the main pom.xml file, once I changed it in the storage-configuration.yml it worked (mostly - there were a few gateway time-outs, but I assume that is because I am running the queries from the US). Thanks for getting back to me so quickly. Simon

j-coll commented 9 years ago

Wonderful!

Any case, if you want to use a different set of configuration variables, you can also create a maven profile with your configuration in ~/.m2/settings.xml instead of modify the configuration files. Of course, you can always modify the configuration by hand. Please, find more information about this in the README.

Jacobo