search

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.
Apache License 2.0
166 stars 97 forks source link

Error annotating variants with Cellbase #233

Closed simonjwhite closed 8 years ago

simonjwhite commented 8 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 gland","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.010898923},{"experimentalFactor":"organism_part","factorValue":"lung","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.004141574},{"experimentalFactor":"groups_96","factorValue":"frontal cortex","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.0},{"experimentalFactor":"blood_nonblood_meta_groups","factorValue":"blood","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":3.920416E-39},{"experimentalFactor":"groups_96","factorValue":"lymph node","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":0.03488875},{"experimentalFactor":"groups_96","factorValue":"cerebellum","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":1.0562018E-19},{"experimentalFactor":"organism_part","factorValue":"cord blood","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":0.0048787384},{"experimentalFactor":"organism_part","factorValue":"eye","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.019681012},{"experimentalFactor":"organism_part","factorValue":"hypothalamus","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.007690713},{"experimentalFactor":"groups_369","factorValue":"amygdala","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":1.0201247E-5},{"experimentalFactor":"groups_96","factorValue":"prostate gland","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.0064071333},{"experimentalFactor":"groups_96","factorValue":"smooth muscle","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.006556711},{"experimentalFactor":"groups_369","factorValue":"myometrium","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":3.2872748E-7},{"experimentalFactor":"groups_369","factorValue":"prefrontal cortex","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":1.4304802E-4},{"experimentalFactor":"organism_part","factorValue":"esophagus","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.011358815},{"experimentalFactor":"organism_part","factorValue":"small intestine","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":5.462758E-12},{"experimentalFactor":"groups_369","factorValue":"hippocampus CA1","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":5.2537103E-11},{"experimentalFactor":"groups_96","factorValue":"hypothalamus","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.0013453476},{"experimentalFactor":"organism_part","factorValue":"blood","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":2.6568057E-7},{"experimentalFactor":"groups_96","factorValue":"myometrium","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":3.2017406E-6},{"experimentalFactor":"groups_369","factorValue":"hypothalamus","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.0025954999},{"experimentalFactor":"organism_part","factorValue":"hippocampus CA1","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":9.314051E-9},{"experimentalFactor":"groups_96","factorValue":"skeletal muscle","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.0023591414},{"experimentalFactor":"organism_part","factorValue":"palatine tonsil","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":0.004168082},{"experimentalFactor":"groups_369","factorValue":"blood","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":8.322317E-9},{"experimentalFactor":"organism_part","factorValue":"skin","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":5.8787754E-7},{"experimentalFactor":"groups_369","factorValue":"skeletal muscle","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.0043852506},{"experimentalFactor":"organism_part","factorValue":"conjunctiva","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.01150032},{"experimentalFactor":"organism_part","factorValue":"ovary","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":0.00916053},{"experimentalFactor":"groups_96","factorValue":"blood","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":2.328186E-7},{"experimentalFactor":"groups_369","factorValue":"heart","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":4.322007E-11},{"experimentalFactor":"organism_part","factorValue":"colon mucosa","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.011452695},{"experimentalFactor":"groups_96","factorValue":"heart","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":3.0961635E-9},{"experimentalFactor":"organism_part","factorValue":"smooth muscle","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.022158494},{"experimentalFactor":"organism_part","factorValue":"thymus","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":1.0482565E-4},{"experimentalFactor":"groups_369","factorValue":"smooth muscle","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.0108603835},{"experimentalFactor":"organism_part","factorValue":"thyroid","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.0119763315},{"experimentalFactor":"organism_part","factorValue":"placental basal plate","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":2.906315E-7},{"experimentalFactor":"groups_96","factorValue":"brain","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.0},{"experimentalFactor":"organism_part","factorValue":"atrial myocardium","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":1.8521163E-5},{"experimentalFactor":"organism_part","factorValue":"colon","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":0.01348853},{"experimentalFactor":"groups_369","factorValue":"small intestine","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":1.1344212E-17},{"experimentalFactor":"organism_part","factorValue":"mammary gland","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":5.840518E-20},{"experimentalFactor":"groups_369","factorValue":"bone","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":0.021365492},{"experimentalFactor":"organism_part","factorValue":"quadriceps","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.011067246},{"experimentalFactor":"organism_part","factorValue":"myometrium","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":4.428901E-4},{"experimentalFactor":"organism_part","factorValue":"larynx","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":7.112255E-4},{"experimentalFactor":"organism_part","factorValue":"uterus","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":4.637579E-10},{"experimentalFactor":"organism_part","factorValue":"hypopharynx","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":0.007869678},{"experimentalFactor":"groups_369","factorValue":"cerebellum","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":2.1194655E-21},{"experimentalFactor":"groups_369","factorValue":"caudate nucleus","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.0},{"experimentalFactor":"metagroups_6","factorValue":"brain","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.0},{"experimentalFactor":"organism_part","factorValue":"umbilical vein","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":2.2812728E-4},{"experimentalFactor":"organism_part","factorValue":"cardiac ventricle","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":2.1669506E-9},{"experimentalFactor":"organism_part","factorValue":"amygdala","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":5.301369E-4},{"experimentalFactor":"organism_part","factorValue":"bone","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":1.8112316E-6},{"experimentalFactor":"groups_369","factorValue":"frontal cortex","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.0},{"experimentalFactor":"groups_369","factorValue":"lymph node","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":0.027240021},{"experimentalFactor":"groups_4_blood","factorValue":"blood","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":1.7358148E-31},{"experimentalFactor":"organism_part","factorValue":"brain","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":3.5239055E-34},{"experimentalFactor":"groups_96","factorValue":"caudate nucleus","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.0},{"experimentalFactor":"organism_part","factorValue":"cervix","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":0.002895816},{"experimentalFactor":"metagroups_6","factorValue":"muscle","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":3.5064295E-24},{"experimentalFactor":"organism_part","factorValue":"liver","experimentId":"E-MTAB-62","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":1.1059866E-19},{"experimentalFactor":"organism_part","factorValue":"prostate","experimentId":"E-GEOD-24283","technologyPlatform":"A-ENST-3","expression":"DOWN","pvalue":9.751741E-8},{"experimentalFactor":"organism_part","factorValue":"brain","experimentId":"E-GEOD-24283","technologyPlatform":"A-ENST-3","expression":"DOWN","pvalue":6.9493864E-5},{"experimentalFactor":"organism_part","factorValue":"pons","experimentId":"E-AFMX-5","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":1.0493798E-5},{"experimentalFactor":"organism_part","factorValue":"cingulate cortex","experimentId":"E-AFMX-5","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.008962828},{"experimentalFactor":"organism_part","factorValue":"temporal lobe","experimentId":"E-AFMX-5","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":7.650093E-6},{"experimentalFactor":"organism_part","factorValue":"brain","experimentId":"E-AFMX-5","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.0044446397},{"experimentalFactor":"organism_part","factorValue":"trigeminal ganglion","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"UP","pvalue":3.6145074E-29},{"experimentalFactor":"organism_part","factorValue":"parietal lobe","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"UP","pvalue":1.8198696E-17},{"experimentalFactor":"organism_part","factorValue":"corpus callosum","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"DOWN","pvalue":0.0011962478},{"experimentalFactor":"organism_part","factorValue":"subthalamic nucleus","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"DOWN","pvalue":0.03669682},{"experimentalFactor":"organism_part","factorValue":"midbrain","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"UP","pvalue":0.016080316},{"experimentalFactor":"organism_part","factorValue":"salivary gland","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"DOWN","pvalue":0.016316954},{"experimentalFactor":"organism_part","factorValue":"amygdala","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"UP","pvalue":2.1735589E-20},{"experimentalFactor":"organism_part","factorValue":"dorsal root ganglion","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"UP","pvalue":1.07452E-40},{"experimentalFactor":"organism_part","factorValue":"ventral tegmental area","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"UP","pvalue":0.030394962},{"experimentalFactor":"organism_part","factorValue":"pituitary gland","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"DOWN","pvalue":4.6878317E-4},{"experimentalFactor":"organism_part","factorValue":"adrenal gland cortex","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"DOWN","pvalue":0.0028168317},{"experimentalFactor":"organism_part","factorValue":"spleen","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"DOWN","pvalue":3.1986454E-7},{"experimentalFactor":"organism_part","factorValue":"hypothalamus","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"UP","pvalue":2.957232E-5},{"experimentalFactor":"organism_part","factorValue":"medulla","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"UP","pvalue":0.022821678},{"experimentalFactor":"organism_part","factorValue":"cerebellum","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"UP","pvalue":1.9890683E-6},{"experimentalFactor":"organism_part","factorValue":"temporal lobe","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"UP","pvalue":8.697504E-12},{"experimentalFactor":"organism_part","factorValue":"thalamus","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"UP","pvalue":0.001924714},{"experimentalFactor":"organism_part","factorValue":"tonsil","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"DOWN","pvalue":5.4380263E-5},{"experimentalFactor":"organism_part","factorValue":"skeletal muscle","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"DOWN","pvalue":1.8157704E-9},{"experimentalFactor":"organism_part","factorValue":"ovary","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"DOWN","pvalue":0.025070164},{"experimentalFactor":"organism_part","factorValue":"adipose tissue","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"DOWN","pvalue":0.044618092},{"experimentalFactor":"organism_part","factorValue":"lymph node","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"DOWN","pvalue":0.0101385545},{"experimentalFactor":"organism_part","factorValue":"cerebral cortex","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"UP","pvalue":1.2851551E-9},{"experimentalFactor":"organism_part","factorValue":"occipital lobe","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"UP","pvalue":5.3948424E-6},{"experimentalFactor":"organism_part","factorValue":"spinal cord","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"DOWN","pvalue":0.0202222},{"experimentalFactor":"organism_part","factorValue":"substantia nigra","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"UP","pvalue":8.5401733E-4},{"experimentalFactor":"organism_part","factorValue":"frontal lobe","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"UP","pvalue":1.4257589E-12},{"experimentalFactor":"organism_part","factorValue":"hippocampus","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"UP","pvalue":1.7178609E-22},{"experimentalFactor":"organism_part","factorValue":"heart ventricle","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"DOWN","pvalue":0.012170144},{"experimentalFactor":"organism_part","factorValue":"liver","experimentId":"E-GEOD-3526","technologyPlatform":"A-AFFY-44","expression":"DOWN","pvalue":2.0681804E-5},{"experimentalFactor":"organism_part","factorValue":"cervix","experimentId":"E-GEOD-20081","technologyPlatform":"A-AFFY-44","expression":"UP","pvalue":2.182943E-6},{"experimentalFactor":"organism_part","factorValue":"mammary gland","experimentId":"E-GEOD-20081","technologyPlatform":"A-AFFY-44","expression":"DOWN","pvalue":2.182943E-6},{"experimentalFactor":"material_type","factorValue":"organism_part","experimentId":"E-GEOD-9171","technologyPlatform":"A-AFFY-44","expression":"UP","pvalue":0.0035735746},{"experimentalFactor":"material_type","factorValue":"organism_part","experimentId":"E-GEOD-9171","technologyPlatform":"A-AFFY-44","expression":"UP","pvalue":0.0035735746},{"experimentalFactor":"organism_part","factorValue":"prostate","experimentId":"E-GEOD-9196","technologyPlatform":"A-AFFY-44","expression":"DOWN","pvalue":0.0016715428},{"experimentalFactor":"organism_part","factorValue":"peripheral blood","experimentId":"E-GEOD-9196","technologyPlatform":"A-AFFY-44","expression":"DOWN","pvalue":6.9572014E-4},{"experimentalFactor":"cell_type","factorValue":"native skin","experimentId":"E-GEOD-3204","technologyPlatform":"A-AFFY-33","expression":"DOWN","pvalue":0.032281887},{"experimentalFactor":"organism_part","factorValue":"pons","experimentId":"E-TABM-145","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":5.556087E-5},{"experimentalFactor":"organism_part","factorValue":"cingulate cortex","experimentId":"E-TABM-145","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.019853633},{"experimentalFactor":"organism_part","factorValue":"temporal lobe","experimentId":"E-TABM-145","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":4.1996653E-5},{"experimentalFactor":"organism_part","factorValue":"brain","experimentId":"E-TABM-145","technologyPlatform":"A-AFFY-33","expression":"UP","pvalue":0.010909509},{"experimentalFactor":"organism_part","factorValue":"hippocampus","experimentId":"E-GEOD-9770","technologyPlatform":"A-AFFY-44","expression":"UP","pvalue":0.001992396},{"experimentalFactor":"organism_part","factorValue":"prostate","experimentId":"E-MTAB-513","technologyPlatform":"A-ENST-3","expression":"UP","pvalue":0.012241327},{"experimentalFactor":"organism_part","factorValue":"adipose","experimentId":"E-MTAB-513","technologyPlatform":"A-ENST-3","expression":"UP","pvalue":0.009908562},{"experimentalFactor":"organism_part","factorValue":"trigeminal 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 8 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 8 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 8 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 8 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