sqlalchemy.exc.ProgrammingError: (sqlite3.ProgrammingError) You must not use 8-bit bytestrings ...

[hoppmann]

Hi,

i tried to update my GEMINI DB with Alamut annotations. For some of the VCF-files this worked rather fine, but for some I acountered this issue.

preparing bed file preparing variables Updating database WARNING: Column "(rsId)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gene)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_geneId)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_geneDesc)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_goBioProcess)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_goCellComp)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_goMolFunc)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_transcript)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_strand)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_transLen)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_cdsLen)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_protein)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_Uniprot)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_varType)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_codingEffect)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_varLocation)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_assembly)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gDNAstart)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gDNAend)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gNomen)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_cDNAstart)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_cDNAend)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_cNomen)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_pNomen)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_alt_pNomen)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_exon)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_intron)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_omimId)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_distNearestSS)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_nearestSSType)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_wtSSFScore)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_wtMaxEntScore)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_wtNNSScore)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_wtGSScore)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_wtHSFScore)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_varSSFScore)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_varMaxEntScore)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_varNNSScore)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_varGSScore)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_varHSFScore)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_nearestSSChange)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_localSpliceEffect)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_localSS_pos)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_localSS_wtMaxEntScore)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_localSS_wtNNSScore)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_localSS_wtSSFScore)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_localSS_varMaxEntScore)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_localSS_varNNSScore)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_localSS_varSSFScore)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_branchPointPos)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_branchPointChange)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_proteinDomain1)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_proteinDomain2)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_proteinDomain3)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_proteinDomain4)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_rsId)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_rsValidated)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_rsSuspect)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_rsValidations)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_rsValidationNumber)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_rsAncestralAllele)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_rsHeterozygosity)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_rsClinicalSignificance)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_rsMAF)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_rsMAFAllele)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_rsMAFCount)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_1000g_AF)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_1000g_AFR_AF)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_1000g_SAS_AF)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_1000g_EAS_AF)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_1000g_EUR_AF)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_1000g_AMR_AF)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadAltFreq_all)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadAltFreq_afr)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadAltFreq_amr)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadAltFreq_asj)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadAltFreq_eas)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadAltFreq_sas)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadAltFreq_nfe)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadAltFreq_fin)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadAltFreq_oth)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadAltCount_all)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadAltCount_afr)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadAltCount_amr)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadAltCount_asj)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadAltCount_eas)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadAltCount_sas)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadAltCount_nfe)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadAltCount_fin)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadAltCount_oth)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadTotalCount_all)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadTotalCount_afr)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadTotalCount_amr)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadTotalCount_asj)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadTotalCount_eas)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadTotalCount_sas)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadTotalCount_nfe)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadTotalCount_fin)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadTotalCount_oth)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHomFreq_all)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHomFreq_afr)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHomFreq_amr)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHomFreq_asj)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHomFreq_eas)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHomFreq_sas)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHomFreq_nfe)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHomFreq_fin)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHomFreq_oth)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHomCount_all)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHomCount_afr)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHomCount_amr)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHomCount_asj)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHomCount_eas)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHomCount_sas)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHomCount_nfe)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHomCount_fin)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHomCount_oth)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHetCount_all)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHetCount_afr)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHetCount_amr)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHetCount_asj)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHetCount_eas)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHetCount_sas)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHetCount_nfe)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHetCount_fin)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHetCount_oth)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHemCount_all)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHemCount_afr)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHemCount_amr)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHemCount_asj)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHemCount_eas)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHemCount_sas)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHemCount_nfe)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHemCount_fin)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadHemCount_oth)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadFilter)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadReadDepth)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_gnomadOrigin)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_espRefEACount)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_espRefAACount)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_espRefAllCount)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_espAltEACount)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_espAltAACount)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_espAltAllCount)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_espEAMAF)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_espAAMAF)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_espAllMAF)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_espEAAAF)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_espAAAAF)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_espAllAAF)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_espAvgReadDepth)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_clinVarIds)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_clinVarOrigins)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_clinVarMethods)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_clinVarClinSignifs)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_clinVarReviewStatus)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_clinVarPhenotypes)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_hgmdId)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_hgmdPhenotype)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_hgmdPubMedId)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_hgmdSubCategory)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_cosmicIds)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_cosmicTissues)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_cosmicFreqs)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_cosmicSampleCounts)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_insNucs)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_delNucs)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_substType)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_wtNuc)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_varNuc)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_nucChange)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_phastCons)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_phyloP)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_wtAA_1)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_wtAA_3)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_wtCodon)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_wtCodonFreq)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_varAA_1)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_varAA_3)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_varCodon)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_varCodonFreq)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_posAA)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_nOrthos)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_conservedOrthos)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_conservedDistSpecies)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_BLOSUM45)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_BLOSUM62)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_BLOSUM80)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_wtAAcomposition)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_varAAcomposition)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_wtAApolarity)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_varAApolarity)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_wtAAvolume)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_varAAvolume)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_granthamDist)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_AGVGDclass)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_AGVGDgv)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_AGVGDgd)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_SIFTprediction)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_SIFTweight)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_SIFTmedian)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_MAPPprediction)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_MAPPpValue)" already exists in variants table. Overwriting values. WARNING: Column "(alamut_MAPPpValueMedian)" already exists in variants table. Overwriting values. updated 5001 variants updated 10002 variants Traceback (most recent call last): File "/data/ngs/bin/gemini/anaconda/bin/gemini", line 7, in gemini_main.main() File "/data/ngs/bin/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1244, in main args.func(parser, args) File "/data/ngs/bin/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 637, in annotate_fn gemini_annotate.annotate(parser, args) File "/data/ngs/bin/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_annotate.py", line 363, in annotate annotate_variants_extract(args, conn, metadata, col_names, col_types, col_ops, col_idxs) File "/data/ngs/bin/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_annotate.py", line 283, in annotate_variants_extract col_names, col_types, col_ops) File "/data/ngs/bin/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_annotate.py", line 116, in _annotate_variants _update_variants(metadata, to_update, col_names, cursor) File "/data/ngs/bin/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_annotate.py", line 137, in _update_variants cursor.execute(stmt, [mkdict(v) for v in to_update]) File "/data/ngs/bin/gemini/anaconda/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 914, in execute return meth(self, multiparams, params) File "/data/ngs/bin/gemini/anaconda/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection return connection._execute_clauseelement(self, multiparams, params) File "/data/ngs/bin/gemini/anaconda/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1010, in _execute_clauseelement compiled_sql, distilled_params File "/data/ngs/bin/gemini/anaconda/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1146, in _execute_context context) File "/data/ngs/bin/gemini/anaconda/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1341, in _handle_dbapi_exception exc_info File "/data/ngs/bin/gemini/anaconda/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause reraise(type(exception), exception, tb=exc_tb, cause=cause) File "/data/ngs/bin/gemini/anaconda/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1116, in _execute_context context) File "/data/ngs/bin/gemini/anaconda/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 447, in do_executemany cursor.executemany(statement, parameters) sqlalchemy.exc.ProgrammingError: (sqlite3.ProgrammingError) You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings. [SQL: u'UPDATE variants SET "rsId"=?, alamut_gene=?, "alamut_geneId"=?, "alamut_geneDesc"=?, "alamut_goBioProcess"=?, "alamut_goCellComp"=?, "alamut_goMolFunc"=?, alamut_transcript=?, alamut_strand=?, "alamut_transLen"=?, "alamut_cdsLen"=?, alamut_protein=?, "alamut_Uniprot"=?, "alamut_varType"=?, "alamut_codingEffect"=?, "alamut_varLocation"=?, alamut_assembly=?, "alamut_gDNAstart"=?, "alamut_gDNAend"=?, "alamut_gNomen"=?, "alamut_cDNAstart"=?, "alamut_cDNAend"=?, "alamut_cNomen"=?, "alamut_pNomen"=?, "alamut_alt_pNomen"=?, alamut_exon=?, alamut_intron=?, "alamut_omimId"=?, "alamut_distNearestSS"=?, "alamut_nearestSSType"=?, "alamut_wtSSFScore"=?, "alamut_wtMaxEntScore"=?, "alamut_wtNNSScore"=?, "alamut_wtGSScore"=?, "alamut_wtHSFScore"=?, "alamut_varSSFScore"=?, "alamut_varMaxEntScore"=?, "alamut_varNNSScore"=?, "alamut_varGSScore"=?, "alamut_varHSFScore"=?, "alamut_nearestSSChange"=?, "alamut_localSpliceEffect"=?, "alamut_localSS_pos"=?, "alamut_localSS_wtMaxEntScore"=?, "alamut_localSS_wtNNSScore"=?, "alamut_localSS_wtSSFScore"=?, "alamut_localSS_varMaxEntScore"=?, "alamut_localSS_varNNSScore"=?, "alamut_localSS_varSSFScore"=?, "alamut_branchPointPos"=?, "alamut_branchPointChange"=?, "alamut_proteinDomain1"=?, "alamut_proteinDomain2"=?, "alamut_proteinDomain3"=?, "alamut_proteinDomain4"=?, "alamut_rsId"=?, "alamut_rsValidated"=?, "alamut_rsSuspect"=?, "alamut_rsValidations"=?, "alamut_rsValidationNumber"=?, "alamut_rsAncestralAllele"=?, "alamut_rsHeterozygosity"=?, "alamut_rsClinicalSignificance"=?, "alamut_rsMAF"=?, "alamut_rsMAFAllele"=?, "alamut_rsMAFCount"=?, "alamut_1000g_AF"=?, "alamut_1000g_AFR_AF"=?, "alamut_1000g_SAS_AF"=?, "alamut_1000g_EAS_AF"=?, "alamut_1000g_EUR_AF"=?, "alamut_1000g_AMR_AF"=?, "alamut_gnomadAltFreq_all"=?, "alamut_gnomadAltFreq_afr"=?, "alamut_gnomadAltFreq_amr"=?, "alamut_gnomadAltFreq_asj"=?, "alamut_gnomadAltFreq_eas"=?, "alamut_gnomadAltFreq_sas"=?, "alamut_gnomadAltFreq_nfe"=?, "alamut_gnomadAltFreq_fin"=?, "alamut_gnomadAltFreq_oth"=?, "alamut_gnomadAltCount_all"=?, "alamut_gnomadAltCount_afr"=?, "alamut_gnomadAltCount_amr"=?, "alamut_gnomadAltCount_asj"=?, "alamut_gnomadAltCount_eas"=?, "alamut_gnomadAltCount_sas"=?, "alamut_gnomadAltCount_nfe"=?, "alamut_gnomadAltCount_fin"=?, "alamut_gnomadAltCount_oth"=?, "alamut_gnomadTotalCount_all"=?, "alamut_gnomadTotalCount_afr"=?, "alamut_gnomadTotalCount_amr"=?, "alamut_gnomadTotalCount_asj"=?, "alamut_gnomadTotalCount_eas"=?, "alamut_gnomadTotalCount_sas"=?, "alamut_gnomadTotalCount_nfe"=?, "alamut_gnomadTotalCount_fin"=?, "alamut_gnomadTotalCount_oth"=?, "alamut_gnomadHomFreq_all"=?, "alamut_gnomadHomFreq_afr"=?, "alamut_gnomadHomFreq_amr"=?, "alamut_gnomadHomFreq_asj"=?, "alamut_gnomadHomFreq_eas"=?, "alamut_gnomadHomFreq_sas"=?, "alamut_gnomadHomFreq_nfe"=?, "alamut_gnomadHomFreq_fin"=?, "alamut_gnomadHomFreq_oth"=?, "alamut_gnomadHomCount_all"=?, "alamut_gnomadHomCount_afr"=?, "alamut_gnomadHomCount_amr"=?, "alamut_gnomadHomCount_asj"=?, "alamut_gnomadHomCount_eas"=?, "alamut_gnomadHomCount_sas"=?, "alamut_gnomadHomCount_nfe"=?, "alamut_gnomadHomCount_fin"=?, "alamut_gnomadHomCount_oth"=?, "alamut_gnomadHetCount_all"=?, "alamut_gnomadHetCount_afr"=?, "alamut_gnomadHetCount_amr"=?, "alamut_gnomadHetCount_asj"=?, "alamut_gnomadHetCount_eas"=?, "alamut_gnomadHetCount_sas"=?, "alamut_gnomadHetCount_nfe"=?, "alamut_gnomadHetCount_fin"=?, "alamut_gnomadHetCount_oth"=?, "alamut_gnomadHemCount_all"=?, "alamut_gnomadHemCount_afr"=?, "alamut_gnomadHemCount_amr"=?, "alamut_gnomadHemCount_asj"=?, "alamut_gnomadHemCount_eas"=?, "alamut_gnomadHemCount_sas"=?, "alamut_gnomadHemCount_nfe"=?, "alamut_gnomadHemCount_fin"=?, "alamut_gnomadHemCount_oth"=?, "alamut_gnomadFilter"=?, "alamut_gnomadReadDepth"=?, "alamut_gnomadOrigin"=?, "alamut_espRefEACount"=?, "alamut_espRefAACount"=?, "alamut_espRefAllCount"=?, "alamut_espAltEACount"=?, "alamut_espAltAACount"=?, "alamut_espAltAllCount"=?, "alamut_espEAMAF"=?, "alamut_espAAMAF"=?, "alamut_espAllMAF"=?, "alamut_espEAAAF"=?, "alamut_espAAAAF"=?, "alamut_espAllAAF"=?, "alamut_espAvgReadDepth"=?, "alamut_clinVarIds"=?, "alamut_clinVarOrigins"=?, "alamut_clinVarMethods"=?, "alamut_clinVarClinSignifs"=?, "alamut_clinVarReviewStatus"=?, "alamut_clinVarPhenotypes"=?, "alamut_hgmdId"=?, "alamut_hgmdPhenotype"=?, "alamut_hgmdPubMedId"=?, "alamut_hgmdSubCategory"=?, "alamut_cosmicIds"=?, "alamut_cosmicTissues"=?, "alamut_cosmicFreqs"=?, "alamut_cosmicSampleCounts"=?, "alamut_insNucs"=?, "alamut_delNucs"=?, "alamut_substType"=?, "alamut_wtNuc"=?, "alamut_varNuc"=?, "alamut_nucChange"=?, "alamut_phastCons"=?, "alamut_phyloP"=?, "alamut_wtAA_1"=?, "alamut_wtAA_3"=?, "alamut_wtCodon"=?, "alamut_wtCodonFreq"=?, "alamut_varAA_1"=?, "alamut_varAA_3"=?, "alamut_varCodon"=?, "alamut_varCodonFreq"=?, "alamut_posAA"=?, "alamut_nOrthos"=?, "alamut_conservedOrthos"=?, "alamut_conservedDistSpecies"=?, "alamut_BLOSUM45"=?, "alamut_BLOSUM62"=?, "alamut_BLOSUM80"=?, "alamut_wtAAcomposition"=?, "alamut_varAAcomposition"=?, "alamut_wtAApolarity"=?, "alamut_varAApolarity"=?, "alamut_wtAAvolume"=?, "alamut_varAAvolume"=?, "alamut_granthamDist"=?, "alamut_AGVGDclass"=?, "alamut_AGVGDgv"=?, "alamut_AGVGDgd"=?, "alamut_SIFTprediction"=?, "alamut_SIFTweight"=?, "alamut_SIFTmedian"=?, "alamut_MAPPprediction"=?, "alamut_MAPPpValue"=?, "alamut_MAPPpValueMedian"=? WHERE variants.variant_id = ?'] [parameters: (('rs3820097', 'NECTIN4', '19688', 'Nectin cell adhesion molecule 4', 'adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell recognition (GO:0008037)|cell-cell junction organization (GO:0045216)|heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules (GO:0007157)|homophilic cell adhesion via plasma membrane adhesion molecules (GO:0007156)|viral process (GO:0016032)', 'cell-cell adherens junction (GO:0005913)|extracellular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)', 'cell adhesion molecule binding (GO:0050839)|protein binding (GO:0005515)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|receptor binding (GO:0005102)', 'NM_030916.2', '-1', '3502', '1533', 'NP_112178.2', 'Q96NY8', 'substitution', '', 'intron', 'GRCh37', '161049358', '161049358', 'Chr1(GRCh37):g.161049358G>A', '439+22', '439+22', 'NM_030916.2:c.439+22C>T', 'p.?', 'p.?', '2', '2', '609607', '22', "5'", '81.1326', '8.8368', '', '', '90.988', '81.1326', '8.8368', '', '', '90.988', '0', '', '', '', '', '', '', '', '', '', '', '', '', '', '', 'rs3820097', 'yes', 'no', 'Frequency/HapMap/1000G', '3', 'A', '', '', '0.139377', 'G', '698', '0.860623', '0.987100', '0.817000', '0.675600', '0.910500', '0.877500', '0.869762', '0.969199', '0.844596', '0.948174', '0.675708', '0.814160', '0.892415', '0.887145', '0.891234', '223188', '21586', '28571', '9349', '12456', '24529', '105155', '16052', '5490', '256608', '22272', '33828', '9860', '18434', '30128', '117832', '18094', '6160', '0.761075', '0.939296', '0.712073', '0.898174', '0.453401', '0.665295', '0.796524', '0.788659', '0.796429', '97649', '10460', '12044', '4428', '4179', '10022', '46928', '7135', '2453', '27890', '666', '4483', '493', '4098', '4485', '11299', '1782', '584', '0', '0', '0', '0', '0', '0', '0', '0', '0', 'PASS', '0', 'Exomes+Genomes', '754', '113', '867', '7270', '3817', '11087', '0.0939681', '0.0287532', '0.072528', '0.906032', '0.971247', '0.927472', '9', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', 'transition', 'C', 'T', 'C>T', '0.000', '-1.086', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '5210'), ('rs11576830,rs11576830', 'KLHDC9,PFDN2', '28489,8867', 'Kelch domain containing 9,Prefoldin subunit 2', ",'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|positive regulation of cytoskeleton organization (GO:0051495)|protein folding (GO:0006457)", ',cytoplasm (GO:0005737)|extracellular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)', ',protein binding (GO:0005515)|protein binding involved in protein folding (GO:0044183)|unfolded protein binding (GO:0051082)', 'NM_152366.4,NM_012394.3', '1,-1', '1319,642', '1050,465', 'NP_689579.3,NP_036526.2', 'Q8NEP7,Q9UHV9', 'substitution,substitution', 'missense,', 'exon,downstream', 'GRCh37,GRCh37', '161068836,161068836', '161068836,161068836', 'Chr1(GRCh37):g.161068836A>C,Chr1(GRCh37):g.161068836A>C', '511,1637', '511,1637', 'NM_152366.4:c.511A>C,NM_012394.3:c.*1637T>G', 'p.Ser171Arg,p.?', 'p.Ser171Arg,p.?', '1,4', ',', '617375,613466', '-17,1814', "5',3'", '72.1684,79.0926', '5.52661,9.39001', ',', ',', '82.531,84.225', '72.1684,79.0926', '5.52661,9.39001', ',', ',', '82.531,84.225', '0,0', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', 'Galactose oxidase/kelch, beta-propeller,', ',', ',', ',', 'rs11576830,rs11576830', 'yes,yes', 'no,no', 'Frequency/HapMap/1000G,Frequency/HapMap/1000G', '3,3', 'A,A', ',', ',', '0.239217,0.239217', 'C,C', '1198,1198', '0.239217,0.239217', '0.066600,0.066600', '0.193300,0.193300', '0.371000,0.371000', '0.339000,0.339000', '0.296800,0.296800', '0.270907,0.270907', '0.090966,0.090966', '0.311954,0.311954', '0.275277,0.275277', '0.345962,0.345962', '0.203375,0.203375', '0.292029,0.292029', '0.308806,0.308806', '0.303249,0.303249', '68306,68306', '2028,2028', '10496,10496', '2679,2679', '6255,6255', '6087,6087', '34137,34137', '4776,4776', '1848,1848', '252138,252138', '22294,22294', '33646,33646', '9732,9732', '18080,18080', '29930,29930', '116896,116896', '15466,15466', '6094,6094', '0.076982,0.076982', '0.009330,0.009330', '0.098377,0.098377', '0.075216,0.075216', '0.123341,0.123341', '0.039559,0.039559', '0.083151,0.083151', '0.094401,0.094401', '0.092878,0.092878', '9705,9705', '104,104', '1655,1655', '366,366', '1115,1115', '592,592', '4860,4860', '730,730', '283,283', '48896,48896', '1820,1820', '7186,7186', '1947,1947', '4025,4025', '4903,4903', '24417,24417', '3316,3316', '1282,1282', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', 'PASS,PASS', '0,0', 'Exomes+Genomes,Exomes+Genomes', '6142,6142', '3983,3983', '10125,10125', '2416,2416', '407,407', '2823,2823', '0.282309,0.282309', '0.0927107,0.0927107', '0.218026,0.218026', '0.282309,0.282309', '0.0927107,0.0927107', '0.218026,0.218026', '17,17', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', 'COSM424364,COSM424364', 'Oesophagus,Oesophagus', '0.000712,0.000712', '1405,1405', ',', ',', 'transversion,transversion', 'A,T', 'C,G', 'A>C,T>G', '0.000,0.000', '-1.247,-1.247', 'S,', 'Ser,', 'AGC,', '0.243,', 'R,', 'Arg,', 'CGC,', '0.190,', '171,', '11,', '7,', 'Frog,', '-1,', '-1,', '-2,', '1.42,', '0.65,', '9.2,', '10.5,', '32,', '124,', '110,', 'C0,', '135.70,', '0.00,', 'Tolerated,', '0.26,', '3.78,', 'good,', '1.955E-1,', '0.07016,', '5211'), ('rs76502631,rs76502631', 'NIT1,PFDN2', '7828,8867', 'Nitrilase 1,Prefoldin subunit 2', "biological_process (GO:0008150)|nitrogen compound metabolic process (GO:0006807),'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|positive regulation of cytoskeleton organization 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'1.8122,10.0684', ',', ',', '78.456,96.907', '71.9755,90.6189', '1.8122,10.0684', ',', ',', '78.456,96.907', '0,0', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', 'rs76502631,rs76502631', 'yes,yes', 'no,no', 'Frequency/1000G,Frequency/1000G', '2,2', 'G,G', ',', ',', '0.009185,0.009185', 'A,A', '46,46', '0.009185,0.009185', '0.000000,0.000000', '0.003100,0.003100', '0.000000,0.000000', '0.026800,0.026800', '0.023100,0.023100', '0.012873,0.012873', '0.004455,0.004455', '0.014906,0.014906', '0.010848,0.010848', '0.000000,0.000000', '0.002891,0.002891', '0.019297,0.019297', '0.008000,0.008000', '0.015330,0.015330', '3564,3564', '107,107', '513,513', '110,110', '0,0', '89,89', '2440,2440', '206,206', '99,99', '276862,276862', '24018,24018', '34416,34416', '10140,10140', '18856,18856', '30782,30782', '126442,126442', '25750,25750', '6458,6458', '0.000202,0.000202', '0.000000,0.000000', '0.000116,0.000116', '0.000394,0.000394', '0.000000,0.000000', '0.000065,0.000065', '0.000348,0.000348', '0.000000,0.000000', '0.000310,0.000310', '28,28', '0,0', '2,2', '2,2', '0,0', '1,1', '22,22', '0,0', '1,1', '3508,3508', '107,107', '509,509', '106,106', '0,0', '87,87', '2396,2396', '206,206', '97,97', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', 'PASS,PASS', '0,0', 'Exomes+Genomes,Exomes+Genomes', '8413,8413', '4386,4386', '12799,12799', '187,187', '20,20', '207,207', '0.0217442,0.0217442', '0.00453926,0.00453926', '0.0159157,0.0159157', '0.0217442,0.0217442', '0.00453926,0.00453926', '0.0159157,0.0159157', '43,43', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', 'transition,transition', 'G,C', 'A,T', 'G>A,C>T', '0.039,0.039', '0.851,0.851', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', '5212'), ('rs191022081,rs191022081', 'NIT1,PFDN2', '7828,8867', 'Nitrilase 1,Prefoldin subunit 2', "biological_process (GO:0008150)|nitrogen compound metabolic process (GO:0006807),'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|positive regulation of cytoskeleton organization (GO:0051495)|protein folding (GO:0006457)", 'extracellular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634),cytoplasm (GO:0005737)|extracellular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)', 'hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds (GO:0016810)|nitrilase activity (GO:0000257),protein binding (GO:0005515)|protein binding involved in protein folding (GO:0044183)|unfolded protein binding (GO:0051082)', 'NM_005600.2,NM_012394.3', '1,-1', '1518,642', '984,465', 'NP_005591.1,NP_036526.2', 'Q86X76,Q9UHV9', 'substitution,substitution', ',', 'intron,upstream', 'GRCh37,GRCh37', '161088365,161088365', '161088365,161088365', 'Chr1(GRCh37):g.161088365A>G,Chr1(GRCh37):g.161088365A>G', '3-211,-549', '3-211,-549', 'NM_005600.2:c.3-211A>G,NM_012394.3:c.-549T>C', 'p.?,p.?', 'p.?,p.?', '2,1', '1,', '604618,613466', '-211,-624', "3',5'", '83.3571,90.6189', '7.1826,10.0684', ',', ',', '89.508,96.907', '83.3571,90.6189', '7.1826,10.0684', ',', ',', '89.508,96.907', '0,0', ',Cryptic Acceptor Strongly Activated', ',161088362', ',4.52376', ',', ',59.3203', ',5.898', ',', ',65.497', ',', ',', ',', ',', ',', ',', 'rs191022081,rs191022081', 'yes,yes', 'no,no', 'Frequency/1000G,Frequency/1000G', '2,2', 'A,A', ',', ',', '0.000599,0.000599', 'G,G', '3,3', '0.000599,0.000599', '0.000000,0.000000', '0.001000,0.001000', '0.000000,0.000000', '0.002000,0.002000', '0.000000,0.000000', '0.001329,0.001329', '0.000461,0.000461', '0.000203,0.000203', '0.000000,0.000000', '0.000000,0.000000', '0.000044,0.000044', '0.002400,0.002400', '0.003829,0.003829', '0.001070,0.001070', '219,219', '7,7', '5,5', '0,0', '0,0', '1,1', '161,161', '40,40', '5,5', '164756,164756', '15196,15196', '24678,24678', '8388,8388', '11626,11626', '22678,22678', '67072,67072', '10446,10446', '4672,4672', '0.000012,0.000012', '0.000000,0.000000', '0.000000,0.000000', '0.000000,0.000000', '0.000000,0.000000', '0.000000,0.000000', '0.000030,0.000030', '0.000000,0.000000', '0.000000,0.000000', '1,1', '0,0', '0,0', '0,0', '0,0', '0,0', '1,1', '0,0', '0,0', '217,217', '7,7', '5,5', '0,0', '0,0', '1,1', '159,159', '40,40', '5,5', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', 'PASS,PASS', '0,0', 'Exomes+Genomes,Exomes+Genomes', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', 'transition,transition', 'A,T', 'G,C', 'A>G,T>C', '0.000,0.000', '-0.360,-0.360', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', '5213'), ('rs41270017,rs41270017', 'NIT1,PFDN2', '7828,8867', 'Nitrilase 1,Prefoldin subunit 2', "biological_process (GO:0008150)|nitrogen compound metabolic process (GO:0006807),'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|positive regulation of cytoskeleton organization (GO:0051495)|protein folding (GO:0006457)", 'extracellular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634),cytoplasm (GO:0005737)|extracellular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)', 'hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds (GO:0016810)|nitrilase activity (GO:0000257),protein binding (GO:0005515)|protein binding involved in protein folding (GO:0044183)|unfolded protein binding (GO:0051082)', 'NM_005600.2,NM_012394.3', '1,-1', '1518,642', '984,465', 'NP_005591.1,NP_036526.2', 'Q86X76,Q9UHV9', 'substitution,substitution', 'missense,', 'exon,upstream', 'GRCh37,GRCh37', '161088583,161088583', '161088583,161088583', 'Chr1(GRCh37):g.161088583T>G,Chr1(GRCh37):g.161088583T>G', '10,-767', '10,-767', 'NM_005600.2:c.10T>G,NM_012394.3:c.-767A>C', 'p.Phe4Val,p.?', 'p.Phe4Val,p.?', '2,1', ',', '604618,613466', '8,-842', "3',5'", '83.3571,90.6189', '7.1826,10.0684', ',', ',', '89.508,96.907', '83.3571,90.6189', '7.1826,10.0684', ',', ',', '89.508,96.907', '0,0', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', 'rs41270017,rs41270017', 'yes,yes', 'no,no', 'Frequency/1000G,Frequency/1000G', '2,2', 'T,T', ',', ',', '0.092851,0.092851', 'G,G', '465,465', '0.092851,0.092851', '0.106700,0.106700', '0.139100,0.139100', '0.067500,0.067500', '0.073600,0.073600', '0.066300,0.066300', '0.084908,0.084908', '0.114017,0.114017', '0.080490,0.080490', '0.045714,0.045714', '0.061268,0.061268', '0.136508,0.136508', '0.078669,0.078669', '0.067960,0.067960', '0.074985,0.074985', '23534,23534', '2738,2738', '2770,2770', '464,464', '1156,1156', '4202,4202', '9967,9967', '1752,1752', '485,485', '277172,277172', '24014,24014', '34414,34414', '10150,10150', '18868,18868', '30782,30782', '126696,126696', '25780,25780', '6468,6468', '0.007670,0.007670', '0.011660,0.011660', '0.006741,0.006741', '0.002167,0.002167', '0.004346,0.004346', '0.019752,0.019752', '0.005651,0.005651', '0.005586,0.005586', '0.006494,0.006494', '1063,1063', '140,140', '116,116', '11,11', '41,41', '304,304', '358,358', '72,72', '21,21', '21408,21408', '2458,2458', '2538,2538', '442,442', '1074,1074', '3594,3594', '9251,9251', '1608,1608', '443,443', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', 'PASS,PASS', '0,0', 'Exomes+Genomes,Exomes+Genomes', '7919,7919', '3896,3896', '11815,11815', '681,681', '510,510', '1191,1191', '0.079186,0.079186', '0.115751,0.115751', '0.0915731,0.0915731', '0.079186,0.079186', '0.115751,0.115751', '0.0915731,0.0915731', '139,139', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', 'COSM3997016,COSM3997016', 'Haematopoietic and lymphoid tissue,Haematopoietic and lymphoid tissue', '0.000283,0.000283', '3530,3530', ',', ',', 'transversion,transversion', 'T,A', 'G,C', 'T>G,A>C', '0.992,0.992', '0.528,0.528', 'F,', 'Phe,', 'TTC,', '0.546,', 'V,', 'Val,', 'GTC,', '0.240,', '4,', '12,', '6,', 'Cow,', '0,', '-1,', '-2,', '0,', '0,', '5.2,', '5.9,', '132,', '84,', '50,', 'C0,', '353.86,', '0.00,', 'Tolerated,', '0.38,', '4.32,', 'unknown,', '0.0,', '0.0,', '5214'), ('rs41270019,rs41270019', 'NIT1,PFDN2', '7828,8867', 'Nitrilase 1,Prefoldin subunit 2', "biological_process (GO:0008150)|nitrogen compound metabolic process (GO:0006807),'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|positive regulation of cytoskeleton organization (GO:0051495)|protein folding (GO:0006457)", 'extracellular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634),cytoplasm (GO:0005737)|extracellular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)', 'hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds (GO:0016810)|nitrilase activity (GO:0000257),protein binding (GO:0005515)|protein binding involved in protein folding (GO:0044183)|unfolded protein binding (GO:0051082)', 'NM_005600.2,NM_012394.3', '1,-1', '1518,642', '984,465', 'NP_005591.1,NP_036526.2', 'Q86X76,Q9UHV9', 'substitution,substitution', ',', 'intron,upstream', 'GRCh37,GRCh37', '161088695,161088695', '161088695,161088695', 'Chr1(GRCh37):g.161088695A>C,Chr1(GRCh37):g.161088695A>C', '98+24,-879', '98+24,-879', 'NM_005600.2:c.98+24A>C,NM_012394.3:c.-879T>G', 'p.?,p.?', 'p.?,p.?', '2,1', '2,', '604618,613466', '24,-954', "5',5'", '81.9751,90.6189', '8.87834,10.0684', ',', ',', '85.651,96.907', '81.9751,90.6189', '8.87834,10.0684', ',', ',', '85.651,96.907', '0,0', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', 'rs41270019,rs41270019', 'yes,yes', 'no,no', 'Frequency/1000G,Frequency/1000G', '2,2', 'A,A', ',', ',', '0.051118,0.051118', 'C,C', '256,256', '0.051118,0.051118', '0.025000,0.025000', '0.089000,0.089000', '0.029800,0.029800', '0.082500,0.082500', '0.033100,0.033100', '0.052810,0.052810', '0.028376,0.028376', '0.026154,0.026154', '0.050857,0.050857', '0.038686,0.038686', '0.081167,0.081167', '0.062219,0.062219', '0.042255,0.042255', '0.052290,0.052290', '14630,14630', '682,682', '900,900', '516,516', '730,730', '2498,2498', '7883,7883', '1083,1083', '338,338', '277030,277030', '24034,24034', '34412,34412', '10146,10146', '18870,18870', '30776,30776', '126698,126698', '25630,25630', '6464,6464', '0.003169,0.003169', '0.001331,0.001331', '0.001046,0.001046', '0.002563,0.002563', '0.001272,0.001272', '0.007343,0.007343', '0.003725,0.003725', '0.001717,0.001717', '0.002785,0.002785', '439,439', '16,16', '18,18', '13,13', '12,12', '113,113', '236,236', '22,22', '9,9', '13752,13752', '650,650', '864,864', '490,490', '706,706', '2272,2272', '7411,7411', '1039,1039', '320,320', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', 'PASS,PASS', '0,0', 'Exomes+Genomes,Exomes+Genomes', '8066,8066', '4271,4271', '12337,12337', '534,534', '135,135', '669,669', '0.062093,0.062093', '0.03064,0.03064', '0.0514378,0.0514378', '0.062093,0.062093', '0.03064,0.03064', '0.0514378,0.0514378', '101,101', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', 'transversion,transversion', 'A,T', 'C,G', 'A>C,T>G', '0.000,0.000', '-0.037,-0.037', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', '5215'), ('rs111473243,rs111473243,rs111473243', 'DEDD,NIT1,PFDN2', '2755,7828,8867', 'Death effector domain containing,Nitrilase 1,Prefoldin subunit 2', "decidualization (GO:0046697)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901837)|regulation of apoptotic process (GO:0042981)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351),biological_process (GO:0008150)|nitrogen compound metabolic process (GO:0006807),'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|positive regulation of cytoskeleton organization (GO:0051495)|protein folding (GO:0006457)", 'cytoplasm (GO:0005737)|nucleolus (GO:0005730),extracellular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634),cytoplasm (GO:0005737)|extracellular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)', 'DNA binding (GO:0003677)|protein binding (GO:0005515),hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds (GO:0016810)|nitrilase activity (GO:0000257),protein binding (GO:0005515)|protein binding involved in protein folding (GO:0044183)|unfolded protein binding (GO:0051082)', 'NM_032998.2,NM_005600.2,NM_012394.3', '-1,1,-1', '2362,1518,642', '957,984,465', 'NP_127491.1,NP_005591.1,NP_036526.2', 'O75618,Q86X76,Q9UHV9', 'insertion,insertion,insertion', ',,', 'downstream,intron,upstream', 'GRCh37,GRCh37,GRCh37', '161089450,161089452,161089450', '161089451,161089453,161089451', 'Chr1(GRCh37):g.161089450_161089451insTAAACT,Chr1(GRCh37):g.161089452_161089453insAACTTA,Chr1(GRCh37):g.161089450_161089451insTAAACT', '2486,457+50,-1635', '2487,457+51,-1634', 'NM032998.2:c.*24862487insAGTTTA,NM_005600.2:c.457+50_457+51insAACTTA,NM012394.3:c.-1635-1634insAGTTTA', 'p.?,p.?,p.?', 'p.?,p.?,p.?', '6,4,1', ',4,', '606841,604618,613466', '2863,50,-1709', "3',5',5'", '86.6637,90.0021,90.6189', '9.83661,8.68007,10.0684', ',,', ',,', '87.644,95.551,96.907', '86.6637,90.0021,90.6189', '9.83661,8.68007,10.0684', ',,', ',,', '87.644,95.551,96.907', '0,0,0', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', 'rs111473243,rs111473243,rs111473243', 'yes,yes,yes', 'no,no,no', 'Frequency/1000G,Frequency/1000G,Frequency/1000G', '2,2,2', ',,', ',,', ',,', '0.357228,0.357228,0.357228', 'TAAACT,TAAACT,TAAACT', '1789,1789,1789', '0.357228,0.357228,0.357228', '0.239800,0.239800,0.239800', '0.364000,0.364000,0.364000', '0.449400,0.449400,0.449400', '0.400600,0.400600,0.400600', '0.374600,0.374600,0.374600', '0.362388,0.362388,0.362388', '0.264966,0.264966,0.264966', '0.401572,0.401572,0.401572', '0.340973,0.340973,0.340973', '0.417627,0.417627,0.417627', '0.364227,0.364227,0.364227', '0.370332,0.370332,0.370332', '0.324071,0.324071,0.324071', '0.381281,0.381281,0.381281', '97976,97976,97976', '6241,6241,6241', '13488,13488,13488', '3407,3407,3407', '7681,7681,7681', '11098,11098,11098', '45399,45399,45399', '8234,8234,8234', '2428,2428,2428', '270362,270362,270362', '23554,23554,23554', '33588,33588,33588', '9992,9992,9992', '18392,18392,18392', '30470,30470,30470', '122590,122590,122590', '25408,25408,25408', '6368,6368,6368', '0.128886,0.128886,0.128886', '0.065806,0.065806,0.065806', '0.157437,0.157437,0.157437', '0.115292,0.115292,0.115292', '0.174206,0.174206,0.174206', '0.133902,0.133902,0.133902', '0.131087,0.131087,0.131087', '0.102015,0.102015,0.102015', '0.142902,0.142902,0.142902', '17423,17423,17423', '775,775,775', '2644,2644,2644', '576,576,576', '1602,1602,1602', '2040,2040,2040', '8035,8035,8035', '1296,1296,1296', '455,455,455', '63129,63129,63129', '4690,4690,4690', '8200,8200,8200', '2255,2255,2255', '4477,4477,4477', '7018,7018,7018', '29329,29329,29329', '5642,5642,5642', '1518,1518,1518', '0,0,0', '0,0,0', '0,0,0', '0,0,0', '0,0,0', '0,0,0', '0,0,0', '0,0,0', '0,0,0', 'PASS,PASS,PASS', '0,0,0', 'Exomes+Genomes,Exomes+Genomes,Exomes+Genomes', '5208,5208,5208', '3082,3082,3082', '8290,8290,8290', '3004,3004,3004', '1177,1177,1177', '4181,4181,4181', '0.365806,0.365806,0.365806', '0.276356,0.276356,0.276356', '0.335258,0.335258,0.335258', '0.365806,0.365806,0.365806', '0.276356,0.276356,0.276356', '0.335258,0.335258,0.335258', '20,20,20', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', 'AGTTTA,AACTTA,AGTTTA', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', ',,', '5216'), ('rs17389237,rs17389237', 'DEDD,NIT1', '2755,7828', 'Death effector domain containing,Nitrilase 1', 'decidualization (GO:0046697)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901837)|regulation of apoptotic process (GO:0042981)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351),biological_process (GO:0008150)|nitrogen compound metabolic process (GO:0006807)', 'cytoplasm (GO:0005737)|nucleolus (GO:0005730),extracellular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)', 'DNA binding (GO:0003677)|protein binding (GO:0005515),hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds (GO:0016810)|nitrilase activity (GO:0000257)', 'NM_032998.2,NM_005600.2', '-1,1', '2362,1518', '957,984', 'NP_127491.1,NP_005591.1', 'O75618,Q86X76', 'substitution,substitution', ',', 'intron,downstream', 'GRCh37,GRCh37', '161092761,161092761', '161092761,161092761', 'Chr1(GRCh37):g.161092761A>G,Chr1(GRCh37):g.161092761A>G', '580+104,2206', '580+104,2206', 'NM_032998.2:c.580+104T>C,NM_005600.2:c.2206A>G', 'p.?,p.?', 'p.?,p.?', '5,7', '5,', '606841,604618', '104,2473', "5',3'", '79.0531,80.391', '6.12664,5.64414', ',', ',', '90.397,89.566', '79.0531,80.391', '6.12664,5.64414', ',', ',', '90.397,89.566', '0,0', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', 'rs17389237,rs17389237', 'yes,yes', 'no,no', 'Frequency/HapMap/1000G,Frequency/HapMap/1000G', '3,3', 'A,A', ',', ',', '0.092851,0.092851', 'G,G', '465,465', '0.092851,0.092851', '0.106700,0.106700', '0.138000,0.138000', '0.067500,0.067500', '0.074600,0.074600', '0.066300,0.066300', '0.085188,0.085188', '0.113786,0.113786', '0.080596,0.080596', '0.045634,0.045634', '0.061234,0.061234', '0.139140,0.139140', '0.078605,0.078605', '0.067951,0.067951', '0.075410,0.075410', '23543,23543', '2732,2732', '2773,2773', '463,463', '1155,1155', '4283,4283', '9900,9900', '1750,1750', '487,487', '276364,276364', '24010,24010', '34406,34406', '10146,10146', '18862,18862', '30782,30782', '125946,125946', '25754,25754', '6458,6458', '0.007751,0.007751', '0.011662,0.011662', '0.006801,0.006801', '0.002168,0.002168', '0.004347,0.004347', '0.020207,0.020207', '0.005701,0.005701', '0.005514,0.005514', '0.006504,0.006504', '1071,1071', '140,140', '117,117', '11,11', '41,41', '311,311', '359,359', '71,71', '21,21', '21401,21401', '2452,2452', '2539,2539', '441,441', '1073,1073', '3661,3661', '9182,9182', '1608,1608', '445,445', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', 'PASS,PASS', '0,0', 'Exomes+Genomes,Exomes+Genomes', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', 'transition,transition', 'T,A', 'C,G', 'T>C,A>G', '0.000,0.000', '0.205,0.205', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', '5217') ... displaying 10 of 5001 total bound parameter sets ... ('rs144773989,rs144773989', 'RAB6C,RAB6C-AS1', '16525,49278', 'RAB6C, member RAS oncogene family,RAB6C antisense RNA 1', 'Rab protein signal transduction (GO:0032482)|cell cycle process (GO:0022402)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|nucleocytoplasmic transport (GO:0006913)|protein transport (GO:0015031)|regulation of centrosome duplication (GO:0010824)|response to drug (GO:0042493)|retrograde transport, endosome to Golgi (GO:0042147)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264),', 'Golgi apparatus (GO:0005794)|centrosome (GO:0005813)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634),', 'GTP binding (GO:0005525)|GTPase activity (GO:0003924),', 'NM_032144.2,NR_036537.1', '1,-1', '3077,2460', '765,0', 'NP_115520.2,', 'Q9H0N0,', 'substitution,substitution', 'missense,', 'exon,upstream', 'GRCh37,GRCh37', '130738163,130738163', '130738163,130738163', 'Chr2(GRCh37):g.130738163G>A,Chr2(GRCh37):g.130738163G>A', '475,-118', '475,-118', 'NM_032144.2:c.475G>A,NR_036537.1:n.-118C>T', 'p.Ala159Thr,p.?', 'p.Ala159Thr,p.?', '1,1', ',', '612909,', ',-307', ",5'", ',64.9271', ',1.99136', ',', ',', ',68.452', ',64.9271', ',1.99136', ',', ',', ',68.452', ',0', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', 'Small GTPase superfamily,', 'Small GTPase superfamily, ARF/SAR type,', 'Small GTP-binding protein domain,', 'Small GTPase superfamily, Ras type,', 'rs4662674,rs4662674', 'yes,yes', 'no,no', 'Frequency/1000G,Frequency/1000G', '2,2', ',', ',', ',', '0.422923,0.422923', 'G,G', '2118,2118', '0.577077,0.577077', '0.336600,0.336600', '0.671800,0.671800', '0.610100,0.610100', '0.692800,0.692800', '0.685900,0.685900', '0.646037,0.646037', '0.384229,0.384229', '0.679570,0.679570', '0.653990,0.653990', '0.645065,0.645065', '0.660029,0.660029', '0.690890,0.690890', '0.600481,0.600481', '0.663467,0.663467', '178876,178876', '9190,9190', '23384,23384', '6638,6638', '12144,12144', '20317,20317', '87439,87439', '15478,15478', '4286,4286', '276882,276882', '23918,23918', '34410,34410', '10150,10150', '18826,18826', '30782,30782', '126560,126560', '25776,25776', '6460,6460', '0.425228,0.425228', '0.147002,0.147002', '0.463354,0.463354', '0.427586,0.427586', '0.415595,0.415595', '0.440192,0.440192', '0.477133,0.477133', '0.362741,0.362741', '0.437771,0.437771', '58869,58869', '1758,1758', '7972,7972', '2170,2170', '3912,3912', '6775,6775', '30193,30193', '4675,4675', '1414,1414', '61138,61138', '5674,5674', '7440,7440', '2298,2298', '4320,4320', '6767,6767', '27053,27053', '6128,6128', '1458,1458', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', 'PASS,PASS', '0,0', 'Exomes+Genomes,Exomes+Genomes', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', 'COSM3757619|COSM3757619|COSM3757619|COSM3757619|COSM3757619,COSM3757619|COSM3757619|COSM3757619|COSM3757619|COSM3757619', 'Upper aerodigestive tract|Prostate|Large intestine|Haematopoietic and lymphoid tissue|Breast,Upper aerodigestive tract|Prostate|Large intestine|Haematopoietic and lymphoid tissue|Breast', '0.016881|0.001134|0.000448|0.000283|0.000408,0.016881|0.001134|0.000448|0.000283|0.000408', '1244|1764|2231|3530|2453,1244|1764|2231|3530|2453', ',', ',', 'transition,transition', 'G,C', 'A,T', 'G>A,C>T', '0.992,0.992', '0.205,0.205', 'A,', 'Ala,', 'GCT,', '0.263,', 'T,', 'Thr,', 'ACT,', '0.243,', '159,', '12,', '12,', "Baker's yeast,", '0,', '0,', '0,', '0,', '0.71,', '8.1,', '8.6,', '31,', '61,', '58,', 'C55,', '0.00,', '58.02,', 'Deleterious,', '0,', '4.32,', 'bad,', '1.194E-5,', '2.111E-5,', '10395'), ('rs13006246,rs13006246', 'CCDC74B,MED15P9', '25267,44130', 'Coiled-coil domain containing 74B,Mediator complex subunit 15 pseudogene 9', ',', ',', ',', 'NM_207310.2,NR_033903.1', '-1,1', '1553,1835', '1143,0', 'NP_997193.1,', 'Q96LY2,', 'substitution,substitution', 'synonymous,', 'exon,downstream', 'GRCh37,GRCh37', '130897218,130897218', '130897218,130897218', 'Chr2(GRCh37):g.130897218T>C,Chr2(GRCh37):g.130897218T>C', '1053,232', '1053,232', 'NM_207310.2:c.1053A>G,NR_033903.1:n.*232T>C', 'p.Ala351=,p.?', 'p.Ala351Ala,p.?', '8,6', ',', ',', '46,1035', "3',3'", '73.2686,85.9629', '7.04215,6.95247', ',', ',', '84.469,86.503', '73.2686,85.9629', '7.04215,6.95247', ',', ',', '84.469,86.503', '0,0', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', 'rs13006246,rs13006246', 'yes,yes', 'no,no', 'Frequency/1000G,Frequency/1000G', '2,2', ',', ',', ',', '0.109625,0.109625', 'C,C', '549,549', '0.109625,0.109625', '0.025000,0.025000', '0.070600,0.070600', '0.028800,0.028800', '0.286300,0.286300', '0.187300,0.187300', '0.185727,0.185727', '0.055066,0.055066', '0.148275,0.148275', '0.351555,0.351555', '0.029518,0.029518', '0.089323,0.089323', '0.251428,0.251428', '0.189078,0.189078', '0.232783,0.232783', '51095,51095', '1311,1311', '5090,5090', '3550,3550', '556,556', '2744,2744', '31527,31527', '4823,4823', '1494,1494', '275108,275108', '23808,23808', '34328,34328', '10098,10098', '18836,18836', '30720,30720', '125392,125392', '25508,25508', '6418,6418', '0.042907,0.042907', '0.003528,0.003528', '0.024819,0.024819', '0.124381,0.124381', '0.001380,0.001380', '0.010417,0.010417', '0.063497,0.063497', '0.036773,0.036773', '0.057027,0.057027', '5902,5902', '42,42', '426,426', '628,628', '13,13', '160,160', '3981,3981', '469,469', '183,183', '39291,39291', '1227,1227', '4238,4238', '2294,2294', '530,530', '2424,2424', '23565,23565', '3885,3885', '1128,1128', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', '0,0', 'PASS,PASS', '0,0', 'Exomes+Genomes,Exomes+Genomes', '6348,6348', '4109,4109', '10457,10457', '2250,2250', '293,293', '2543,2543', '0.261689,0.261689', '0.0665607,0.0665607', '0.195615,0.195615', '0.261689,0.261689', '0.0665607,0.0665607', '0.195615,0.195615', '37,37', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', 'COSM3757620|COSM3757620,COSM3757620|COSM3757620', 'Large intestine|Kidney,Large intestine|Kidney', '0.000448|0.000578,0.000448|0.000578', '2231|1729,2231|1729', ',', ',', 'transition,transition', 'A,T', 'G,C', 'A>G,T>C', '0.228,0.228', '-2.781,-2.781', 'A,', 'Ala,', 'GCA,', '0.226,', 'A,', 'Ala,', 'GCG,', '0.107,', '351,', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', ',', '10397'))]

My command used for updateing. gemini annotate $db -f $bedFile -a extract -c $ALAMUT_COLS -e $ALAMUT_IDXS -t $ALAMUT_COLTYPES -o $ALAMUT_MODE

Where $ALAMUT_COLS are the collumns I want to add, $ALAMUT_IDX are the corresponding indexes $ALAMUT_COLTYPES is a vector with "text" equal to the number of columns and $ALAMUT_MODE is a vecotr containing "list" equal to the number of columns to add.

Is there a bug, or do I have to do something differently?

Thanks

[brentp]

Can you update to master from git and try again? I have fixed a bug related to this since last release.

[hoppmann]

Hi, thanks for the quick response. I updated GEMINI to version 20.1. But unfortunately this didn't solve the problem. I still get the same error.

Best, Anselm

[brentp]

Can you create a small file that shows the problem? It looks like it's rs11576830 so if you give me that line from your file, along with the header, and whatever you are annotating with, I can resolve.

[hoppmann]

Hi, I tried to get a small dataset with just the erroneous line. But unfortunately I wasn't able to replicate the issue after extracting the corresponding line. I also tried to extract some lines prior and after the stated line in the error message, but still didn't get any error. Then running the big data set again, I regain the error.

What I noticed is that the error message often prints out multiple entries in one line. E.g. in the example above 'rs144773989,rs144773989' or even 'rs28365980,.,rs28365979,rs28365978' in another file. Is this correct? Are entries added in smaller batches, or might it be, that exactly these multiple entries cause the trouble? I have to mention, that these entries don't show up in the file. But further these are consecutive lines in the original file.

Should I still upload a file containing the corresponding lines? I could also provide the big files, if it would help you.

Best, Anselm

[brentp]

you said that you updated to 20.1, but can you try updateding to github master? If that doesn't work then I'll need some way to recreate the problem in order to fix it.

[hoppmann]

Hi,

now I understood what you ment. I updated to the developer version (0.20.2-dev) and so far it seems to work well.

Thanks alot for the help and keep up the great work.

Best, Anselm

[brentp]

great. thanks for following up.