Annotation issue - "No information" when there are many annotations

[mdozmorov]

Standard CNVpytor procedure:

set Q0_range -1 0.5
set p_range 0 0.001
set p_N 0 0.5
set size_range 50000 inf
set dG_range 100000 inf
set print_filename results_joint.xlsx
set annotate
print joint_calls

generates the Excel file with some annotations that seem missing. I'm sorting CNVs by the largest SIZE and the largest CNV difference. The top largest regions are annotated as "No information" while they do overlap many protein-coding genes. hg38 coordinates of such regions:

chr5:82432001-102132000
chr3:32767001-41890000
chr4:114263001-121361000
chr5:70496001-79783000

That's how the annotations are expected to look:

<style> </style>

seqnames	start	end	width	SYMBOL
chr5	82432001	102132000	19700000	ADGRV1;ARRDC3;ARRDC3-AS1;ARSK;CAST;CCNH;CETN3;CHD1;COX7C;EDIL3;EDIL3-DT;ELL2;ERAP1;ERAP2;FAM172A;FAM174A;FAM81B;GLRX;GPR150;GUSBP19;HAPLN1;KIAA0825;LINC00461;LINC01338;LINC01339;LINC01340;LINC01554;LINC01846;LINC01949;LINC02058;LINC02059;LINC02060;LINC02113;LINC02144;LINC02161;LINC02234;LINC02488;LIX1;LIX1-AS1;LNPEP;LOC101929380;LOC101929710;LOC102724637;LOC105379051;LOC105379065;LOC105379066;LOC105379078;LOC105379080;LOC105379082;LOC105379087;LOC105379090;LOC105379091;LOC105379100;LOC107986363;LOC107986432;LOC107986433;LOC107986434;LOC645261;LOC731157;LUCAT1;LYSMD3;MBLAC2;MCTP1;MEF2C;MEF2C-AS1;MEF2C-AS2;MIR2277;MIR3660;MIR3977;MIR4280;MIR548P;MIR583;MIR583HG;MIR9-2;NBPF22P;NR2F1;NR2F1-AS1;PCSK1;POLR3G;POU5F2;RASA1;RFESD;RGMB;RGMB-AS1;RHOBTB3;RIOK2;SCARNA18;SLF1;SNORD138;SPATA9;ST8SIA4;TMEM161B;TMEM161B-DT;TMEM167A;TTC37;VCAN;VCAN-AS1;XRCC4
chr17	66800001	71608000	4808000	ABCA10;ABCA5;ABCA6;ABCA8;ABCA9;ABCA9-AS1;AMZ2;ARHGAP27P2;ARSG;BPTF;C17orf58;CACNG1;CACNG4;CACNG5;CASC17;FAM20A;HELZ;HELZ-AS1;KCNJ16;KCNJ2;KCNJ2-AS1;KPNA2;LINC00674;LINC01028;LINC01482;LINC01483;LINC01497;LOC101928045;LOC105371873;LOC105371880;LOC112267896;MAP2K6;MIR4524A;MIR4524B;MIR548AA2;MIR548D2;MIR635;NOL11;PITPNC1;PRKAR1A;PRKCA;PRO1804;PSMD12;SLC16A6;SNORA38B;WIPI1
chr3	32767001	41890000	9123000	ACAA1;ACVR2B;ACVR2B-AS1;APRG1;ARPP21;CCR4;CCR8;CLASP2;CNOT10;CRTAP;CSRNP1;CTDSPL;CTNNB1;CX3CR1;DCLK3;DLEC1;EIF1B;EIF1B-AS1;ENTPD3;ENTPD3-AS1;EPM2AIP1;EXOG;FBXL2;GLB1;GOLGA4;GOLGA4-AS1;GORASP1;ITGA9;ITGA9-AS1;LINC01811;LINC02033;LOC101928263;LOC102724048;LOC102724104;LOC105377029;LOC105377033;LOC105377035;LOC105377043;LOC105377644;LOC107986042;LOC107986075;LRRFIP2;MIR128-2;MIR26A1;MIR6822;MLH1;MOBP;MYD88;MYRIP;OXSR1;PDCD6IP;PDCD6IP-DT;PLCD1;RPL14;RPSA;SCN10A;SCN11A;SCN5A;SLC22A13;SLC22A14;SLC25A38;SNORA6;SNORA62;STAC;SUSD5;TMPPE;TRANK1;TRIM71;TTC21A;UBE2FP1;UBP1;ULK4;VILL;WDR48;XIRP1;XYLB;ZNF619;ZNF620;ZNF621
chr4	1.14E+08	121361000	7098000	C4orf3;CEP170P1;FABP2;GTF2IP12;LINC01061;LINC01365;LINC01378;LINC02262;LINC02263;LINC02264;LINC02502;LOC101929762;LOC105377383;LOC105377397;LOC107986306;LOC729218;MAD2L1;MAD2L1-DT;METTL14;METTL14-DT;MIR1973;MIR577;MYOZ2;NDNF;NDNF-AS1;NDST3;NDST4;PDE5A;PRDM5;PRSS12;QRFPR;SEC24D;SEPTIN7P14;SNHG8;SNORA24;SYNPO2;TNIP3;TRAM1L1;UGT8;USP53
chr5	70496001	79783000	9287000	AGGF1;ANKDD1B;ANKRA2;ANKRD31;AP3B1;ARHGEF28;ARSB;BHMT;BHMT2;BTF3;CARTPT;CERT1;CMYA5;CRHBP;DMGDH;ENC1;F2R;F2RL1;F2RL2;FAM169A;FCHO2;FOXD1;GCNT4;GFM2;HEXB;HMGCR;HOMER1;IQGAP2;JMY;LHFPL2;LINC01331;LINC01333;LINC01335;LINC01386;LINC02056;LINC02122;LINC02230;LOC101929109;LOC101929154;LOC101929599;LOC105379026;LOC105379028;LOC105379030;LOC105379042;LOC107986383;LOC340090;LOC441086;MAP1B;MIR4803;MIR4804;MRPS27;NCRUPAR;NSA2;OTP;PDE8B;POC5;POLK;PTCD2;S100Z;SCAMP1;SCAMP1-AS1;SNORA47;SV2C;SV2C-AS1;TBCA;TENT2;TMEM171;TMEM174;TNPO1;UTP15;WDR41;ZBED3;ZBED3-AS1;ZNF366

[suvakov]

Thank you for reporting. This is consequence of size limit (5000000bp) in API we are using:
https://rest.ensembl.org/overlap/region/human/chr5:82432001-102132000?content-type=application/json;feature=gene;. We are working on solution.