counts.mrna<- featureCounts(
+   files="tophat_out/accepted_hits.sort.bam", 
+   file.type="BAM",
+   annot="mm10/annotation/mm10.allmrna.gtf",
+   isGTFAnnotationFile=TRUE,
+   GTF.featureType="exon",
+   GTF.attrType="gene_id",
+   useMetaFeatures=TRUE,
+   nthreads=1,
+   isPairedEnd=TRUE,
+   checkFragLength=TRUE
+ )
Processing tophat_out/accepted_hits.sort.bam  ...

Warning: the feature on the 49-th line has zero coordinate or zero lengths


Warning: the feature on the 10401-th line has zero coordinate or zero lengths


Warning: the feature on the 27770-th line has zero coordinate or zero lengths


Warning: the feature on the 29615-th line has zero coordinate or zero lengths


Warning: the feature on the 37989-th line has zero coordinate or zero lengths


Warning: the feature on the 40584-th line has zero coordinate or zero lengths


Warning: the feature on the 41242-th line has zero coordinate or zero lengths


Warning: the feature on the 57425-th line has zero coordinate or zero lengths


Warning: the feature on the 59397-th line has zero coordinate or zero lengths


Warning: the feature on the 70193-th line has zero coordinate or zero lengths


Warning: the feature on the 72721-th line has zero coordinate or zero lengths


Warning: the feature on the 86307-th line has zero coordinate or zero lengths


Warning: the feature on the 98972-th line has zero coordinate or zero lengths


Warning: the feature on the 106763-th line has zero coordinate or zero lengths


Warning: the feature on the 114333-th line has zero coordinate or zero lengths


Warning: the feature on the 126881-th line has zero coordinate or zero lengths


Warning: the feature on the 136646-th line has zero coordinate or zero lengths


Warning: the feature on the 136856-th line has zero coordinate or zero lengths


Warning: the feature on the 142905-th line has zero coordinate or zero lengths


Warning: the feature on the 171600-th line has zero coordinate or zero lengths


Warning: the feature on the 176863-th line has zero coordinate or zero lengths


Warning: the feature on the 186540-th line has zero coordinate or zero lengths


Warning: the feature on the 186543-th line has zero coordinate or zero lengths


Warning: the feature on the 187925-th line has zero coordinate or zero lengths


Warning: the feature on the 191455-th line has zero coordinate or zero lengths


Warning: the feature on the 199897-th line has zero coordinate or zero lengths


Warning: the feature on the 209862-th line has zero coordinate or zero lengths


Warning: the feature on the 212820-th line has zero coordinate or zero lengths


Warning: the feature on the 219198-th line has zero coordinate or zero lengths


Warning: the feature on the 221450-th line has zero coordinate or zero lengths


Warning: the feature on the 225159-th line has zero coordinate or zero lengths


Warning: the feature on the 226617-th line has zero coordinate or zero lengths


Warning: the feature on the 227789-th line has zero coordinate or zero lengths


Warning: the feature on the 238845-th line has zero coordinate or zero lengths


Warning: the feature on the 248931-th line has zero coordinate or zero lengths


Warning: the feature on the 252009-th line has zero coordinate or zero lengths


Warning: the feature on the 252318-th line has zero coordinate or zero lengths


Warning: the feature on the 257932-th line has zero coordinate or zero lengths


Warning: the feature on the 257934-th line has zero coordinate or zero lengths


Warning: the feature on the 260736-th line has zero coordinate or zero lengths


Warning: the feature on the 261532-th line has zero coordinate or zero lengths


Warning: the feature on the 271463-th line has zero coordinate or zero lengths


Warning: the feature on the 277652-th line has zero coordinate or zero lengths


Warning: the feature on the 287026-th line has zero coordinate or zero lengths


Warning: the feature on the 288590-th line has zero coordinate or zero lengths


Warning: the feature on the 292414-th line has zero coordinate or zero lengths


Warning: the feature on the 298390-th line has zero coordinate or zero lengths


Warning: the feature on the 306850-th line has zero coordinate or zero lengths


Warning: the feature on the 313805-th line has zero coordinate or zero lengths


Warning: the feature on the 328655-th line has zero coordinate or zero lengths


Warning: the feature on the 328658-th line has zero coordinate or zero lengths


Warning: the feature on the 343513-th line has zero coordinate or zero lengths


Warning: the feature on the 345025-th line has zero coordinate or zero lengths


Warning: the feature on the 353159-th line has zero coordinate or zero lengths


Warning: the feature on the 355395-th line has zero coordinate or zero lengths


Warning: the feature on the 359271-th line has zero coordinate or zero lengths


Warning: the feature on the 360496-th line has zero coordinate or zero lengths


Warning: the feature on the 361675-th line has zero coordinate or zero lengths


Warning: the feature on the 362380-th line has zero coordinate or zero lengths


Warning: the feature on the 363571-th line has zero coordinate or zero lengths


Warning: the feature on the 370036-th line has zero coordinate or zero lengths


Warning: the feature on the 373485-th line has zero coordinate or zero lengths


Warning: the feature on the 383339-th line has zero coordinate or zero lengths


Warning: the feature on the 384488-th line has zero coordinate or zero lengths


Warning: the feature on the 384759-th line has zero coordinate or zero lengths


Warning: the feature on the 385767-th line has zero coordinate or zero lengths


Warning: the feature on the 394109-th line has zero coordinate or zero lengths


Warning: the feature on the 427921-th line has zero coordinate or zero lengths


Warning: the feature on the 434874-th line has zero coordinate or zero lengths


Warning: the feature on the 439642-th line has zero coordinate or zero lengths


Warning: the feature on the 440022-th line has zero coordinate or zero lengths


Warning: the feature on the 445642-th line has zero coordinate or zero lengths


Warning: the feature on the 448788-th line has zero coordinate or zero lengths


Warning: the feature on the 456377-th line has zero coordinate or zero lengths


Warning: the feature on the 460437-th line has zero coordinate or zero lengths


Warning: the feature on the 462958-th line has zero coordinate or zero lengths


Warning: the feature on the 467451-th line has zero coordinate or zero lengths


Warning: the feature on the 468948-th line has zero coordinate or zero lengths


Warning: the feature on the 476621-th line has zero coordinate or zero lengths


Warning: the feature on the 478020-th line has zero coordinate or zero lengths


Warning: the feature on the 478294-th line has zero coordinate or zero lengths


Warning: the feature on the 483160-th line has zero coordinate or zero lengths


Warning: the feature on the 486231-th line has zero coordinate or zero lengths


Warning: the feature on the 487298-th line has zero coordinate or zero lengths


Warning: the feature on the 499958-th line has zero coordinate or zero lengths


Warning: the feature on the 500124-th line has zero coordinate or zero lengths


Warning: the feature on the 501050-th line has zero coordinate or zero lengths


Warning: the feature on the 504217-th line has zero coordinate or zero lengths


Warning: the feature on the 504252-th line has zero coordinate or zero lengths


Warning: the feature on the 505838-th line has zero coordinate or zero lengths


Warning: the feature on the 517708-th line has zero coordinate or zero lengths


Warning: the feature on the 522696-th line has zero coordinate or zero lengths


Warning: the feature on the 527160-th line has zero coordinate or zero lengths


Warning: the feature on the 530208-th line has zero coordinate or zero lengths


Warning: the feature on the 552669-th line has zero coordinate or zero lengths


Warning: the feature on the 552674-th line has zero coordinate or zero lengths


Warning: the feature on the 561141-th line has zero coordinate or zero lengths


Warning: the feature on the 561154-th line has zero coordinate or zero lengths


Warning: the feature on the 583953-th line has zero coordinate or zero lengths


Warning: the feature on the 602872-th line has zero coordinate or zero lengths


Warning: the feature on the 603927-th line has zero coordinate or zero lengths


Warning: the feature on the 614006-th line has zero coordinate or zero lengths


Warning: the feature on the 614036-th line has zero coordinate or zero lengths


Warning: the feature on the 614206-th line has zero coordinate or zero lengths


Warning: the feature on the 614235-th line has zero coordinate or zero lengths


Warning: the feature on the 619528-th line has zero coordinate or zero lengths


Warning: the feature on the 621831-th line has zero coordinate or zero lengths


Warning: the feature on the 630987-th line has zero coordinate or zero lengths


Warning: the feature on the 635558-th line has zero coordinate or zero lengths


Warning: the feature on the 639675-th line has zero coordinate or zero lengths


Warning: the feature on the 644729-th line has zero coordinate or zero lengths


Warning: the feature on the 654251-th line has zero coordinate or zero lengths


Warning: the feature on the 661438-th line has zero coordinate or zero lengths


Warning: the feature on the 664500-th line has zero coordinate or zero lengths


Warning: the feature on the 667124-th line has zero coordinate or zero lengths


Warning: the feature on the 681819-th line has zero coordinate or zero lengths


Warning: the feature on the 693671-th line has zero coordinate or zero lengths


Warning: the feature on the 703850-th line has zero coordinate or zero lengths


Warning: the feature on the 706029-th line has zero coordinate or zero lengths


Warning: the feature on the 717013-th line has zero coordinate or zero lengths


Warning: the feature on the 720343-th line has zero coordinate or zero lengths


Warning: the feature on the 720953-th line has zero coordinate or zero lengths


Warning: the feature on the 720957-th line has zero coordinate or zero lengths


Warning: the feature on the 732142-th line has zero coordinate or zero lengths


Warning: the feature on the 732174-th line has zero coordinate or zero lengths


Warning: the feature on the 733898-th line has zero coordinate or zero lengths


Warning: the feature on the 736864-th line has zero coordinate or zero lengths


Warning: the feature on the 738359-th line has zero coordinate or zero lengths


Warning: the feature on the 740842-th line has zero coordinate or zero lengths


Warning: the feature on the 742910-th line has zero coordinate or zero lengths


Warning: the feature on the 743059-th line has zero coordinate or zero lengths


Warning: the feature on the 743850-th line has zero coordinate or zero lengths


Warning: the feature on the 747743-th line has zero coordinate or zero lengths


Warning: the feature on the 747832-th line has zero coordinate or zero lengths


Warning: the feature on the 752140-th line has zero coordinate or zero lengths


Warning: the feature on the 757120-th line has zero coordinate or zero lengths


Warning: the feature on the 762673-th line has zero coordinate or zero lengths


Warning: the feature on the 781326-th line has zero coordinate or zero lengths


Warning: the feature on the 782009-th line has zero coordinate or zero lengths


Warning: the feature on the 786394-th line has zero coordinate or zero lengths


Warning: the feature on the 802690-th line has zero coordinate or zero lengths


Warning: the feature on the 812715-th line has zero coordinate or zero lengths


Warning: the feature on the 818004-th line has zero coordinate or zero lengths


Warning: the feature on the 818010-th line has zero coordinate or zero lengths


Warning: the feature on the 819237-th line has zero coordinate or zero lengths


Warning: the feature on the 819822-th line has zero coordinate or zero lengths


Warning: the feature on the 828407-th line has zero coordinate or zero lengths


Warning: the feature on the 842504-th line has zero coordinate or zero lengths


Warning: the feature on the 848562-th line has zero coordinate or zero lengths


Warning: the feature on the 850262-th line has zero coordinate or zero lengths


Warning: the feature on the 850265-th line has zero coordinate or zero lengths


Warning: the feature on the 850845-th line has zero coordinate or zero lengths


Warning: the feature on the 851310-th line has zero coordinate or zero lengths


Warning: the feature on the 851324-th line has zero coordinate or zero lengths


Warning: the feature on the 855244-th line has zero coordinate or zero lengths


Warning: the feature on the 856876-th line has zero coordinate or zero lengths


Warning: the feature on the 858871-th line has zero coordinate or zero lengths


Warning: the feature on the 863851-th line has zero coordinate or zero lengths


Warning: the feature on the 864273-th line has zero coordinate or zero lengths


Warning: the feature on the 867730-th line has zero coordinate or zero lengths


Warning: the feature on the 871010-th line has zero coordinate or zero lengths


Warning: the feature on the 887536-th line has zero coordinate or zero lengths


Warning: the feature on the 896062-th line has zero coordinate or zero lengths


Warning: the feature on the 898550-th line has zero coordinate or zero lengths


Warning: the feature on the 906728-th line has zero coordinate or zero lengths


Warning: the feature on the 908296-th line has zero coordinate or zero lengths


Warning: the feature on the 914407-th line has zero coordinate or zero lengths


Warning: the feature on the 914412-th line has zero coordinate or zero lengths


Warning: the feature on the 914417-th line has zero coordinate or zero lengths


Warning: the feature on the 923760-th line has zero coordinate or zero lengths


Warning: the feature on the 923771-th line has zero coordinate or zero lengths


Warning: the feature on the 936409-th line has zero coordinate or zero lengths


Warning: the feature on the 942211-th line has zero coordinate or zero lengths


Warning: the feature on the 950381-th line has zero coordinate or zero lengths


Warning: the feature on the 965454-th line has zero coordinate or zero lengths


Warning: the feature on the 966643-th line has zero coordinate or zero lengths


Warning: the feature on the 974419-th line has zero coordinate or zero lengths


Warning: the feature on the 976940-th line has zero coordinate or zero lengths


Warning: the feature on the 979924-th line has zero coordinate or zero lengths


Warning: the feature on the 983817-th line has zero coordinate or zero lengths


Warning: the feature on the 993820-th line has zero coordinate or zero lengths


Warning: the feature on the 993821-th line has zero coordinate or zero lengths


Warning: the feature on the 1005890-th line has zero coordinate or zero lengths


Warning: the feature on the 1008162-th line has zero coordinate or zero lengths


Warning: the feature on the 1011809-th line has zero coordinate or zero lengths


Warning: the feature on the 1028123-th line has zero coordinate or zero lengths


Warning: the feature on the 1035351-th line has zero coordinate or zero lengths


Warning: the feature on the 1040672-th line has zero coordinate or zero lengths


Warning: the feature on the 1041135-th line has zero coordinate or zero lengths


Warning: the feature on the 1044352-th line has zero coordinate or zero lengths


Warning: the feature on the 1048907-th line has zero coordinate or zero lengths


Warning: the feature on the 1053255-th line has zero coordinate or zero lengths


Warning: the feature on the 1054137-th line has zero coordinate or zero lengths


Warning: the feature on the 1060657-th line has zero coordinate or zero lengths


Warning: the feature on the 1069025-th line has zero coordinate or zero lengths


Warning: the feature on the 1069036-th line has zero coordinate or zero lengths


Warning: the feature on the 1069112-th line has zero coordinate or zero lengths


Warning: the feature on the 1086370-th line has zero coordinate or zero lengths


Warning: the feature on the 1087071-th line has zero coordinate or zero lengths


Warning: the feature on the 1089728-th line has zero coordinate or zero lengths


Warning: the feature on the 1090058-th line has zero coordinate or zero lengths


Warning: the feature on the 1090957-th line has zero coordinate or zero lengths


Warning: the feature on the 1097818-th line has zero coordinate or zero lengths


Warning: the feature on the 1098283-th line has zero coordinate or zero lengths


Warning: the feature on the 1103001-th line has zero coordinate or zero lengths


Warning: the feature on the 1104780-th line has zero coordinate or zero lengths


Warning: the feature on the 1111974-th line has zero coordinate or zero lengths


Warning: the feature on the 1122248-th line has zero coordinate or zero lengths


Warning: the feature on the 1122334-th line has zero coordinate or zero lengths


Warning: the feature on the 1122354-th line has zero coordinate or zero lengths


Warning: the feature on the 1122607-th line has zero coordinate or zero lengths


Warning: the feature on the 1122856-th line has zero coordinate or zero lengths


Warning: the feature on the 1122905-th line has zero coordinate or zero lengths


Warning: the feature on the 1123176-th line has zero coordinate or zero lengths


Warning: the feature on the 1123283-th line has zero coordinate or zero lengths


Warning: the feature on the 1123337-th line has zero coordinate or zero lengths


Warning: the feature on the 1123341-th line has zero coordinate or zero lengths


Warning: the feature on the 1123345-th line has zero coordinate or zero lengths


Warning: the feature on the 1123363-th line has zero coordinate or zero lengths


Warning: the feature on the 1123839-th line has zero coordinate or zero lengths


Warning: the feature on the 1124065-th line has zero coordinate or zero lengths


Warning: the feature on the 1129703-th line has zero coordinate or zero lengths


Warning: the feature on the 1137812-th line has zero coordinate or zero lengths


Warning: the feature on the 1138496-th line has zero coordinate or zero lengths


Warning: the feature on the 1139085-th line has zero coordinate or zero lengths


Warning: the feature on the 1140274-th line has zero coordinate or zero lengths


Warning: the feature on the 1141943-th line has zero coordinate or zero lengths


Warning: the feature on the 1142316-th line has zero coordinate or zero lengths


Warning: the feature on the 1142320-th line has zero coordinate or zero lengths


Warning: the feature on the 1142325-th line has zero coordinate or zero lengths


Warning: the feature on the 1142330-th line has zero coordinate or zero lengths


Warning: the feature on the 1142334-th line has zero coordinate or zero lengths


Warning: the feature on the 1142551-th line has zero coordinate or zero lengths


Warning: the feature on the 1142861-th line has zero coordinate or zero lengths


Warning: the feature on the 1143127-th line has zero coordinate or zero lengths


Warning: the feature on the 1143480-th line has zero coordinate or zero lengths


Warning: the feature on the 1143489-th line has zero coordinate or zero lengths


Warning: the feature on the 1143494-th line has zero coordinate or zero lengths


Warning: the feature on the 1143538-th line has zero coordinate or zero lengths


Warning: the feature on the 1143710-th line has zero coordinate or zero lengths


Warning: the feature on the 1144257-th line has zero coordinate or zero lengths


Warning: the feature on the 1144364-th line has zero coordinate or zero lengths


Warning: the feature on the 1145381-th line has zero coordinate or zero lengths


Warning: the feature on the 1145680-th line has zero coordinate or zero lengths


Warning: the feature on the 1145744-th line has zero coordinate or zero lengths


Warning: the feature on the 1145910-th line has zero coordinate or zero lengths


Warning: the feature on the 1145915-th line has zero coordinate or zero lengths


Warning: the feature on the 1152427-th line has zero coordinate or zero lengths


Warning: the feature on the 1162256-th line has zero coordinate or zero lengths


Warning: the feature on the 1166641-th line has zero coordinate or zero lengths


Warning: the feature on the 1168106-th line has zero coordinate or zero lengths


Warning: the feature on the 1175646-th line has zero coordinate or zero lengths


Warning: the feature on the 1179275-th line has zero coordinate or zero lengths


Warning: the feature on the 1180645-th line has zero coordinate or zero lengths


Warning: the feature on the 1183568-th line has zero coordinate or zero lengths


Warning: the feature on the 1195813-th line has zero coordinate or zero lengths


Warning: the feature on the 1198147-th line has zero coordinate or zero lengths


Warning: the feature on the 1207175-th line has zero coordinate or zero lengths


Warning: the feature on the 1208083-th line has zero coordinate or zero lengths


Warning: the feature on the 1226035-th line has zero coordinate or zero lengths


Warning: the feature on the 1232610-th line has zero coordinate or zero lengths


Warning: the feature on the 1234976-th line has zero coordinate or zero lengths


Warning: the feature on the 1238282-th line has zero coordinate or zero lengths


Warning: the feature on the 1241639-th line has zero coordinate or zero lengths


Warning: the feature on the 1248961-th line has zero coordinate or zero lengths


Warning: the feature on the 1258345-th line has zero coordinate or zero lengths


Warning: the feature on the 1258438-th line has zero coordinate or zero lengths


Warning: the feature on the 1266185-th line has zero coordinate or zero lengths


Warning: the feature on the 1293826-th line has zero coordinate or zero lengths


Warning: the feature on the 1297969-th line has zero coordinate or zero lengths


Warning: the feature on the 1308101-th line has zero coordinate or zero lengths


Warning: the feature on the 1308952-th line has zero coordinate or zero lengths


Warning: the feature on the 1319334-th line has zero coordinate or zero lengths


Warning: the feature on the 1322683-th line has zero coordinate or zero lengths


Warning: the feature on the 1330898-th line has zero coordinate or zero lengths


Warning: the feature on the 1352895-th line has zero coordinate or zero lengths


Warning: the feature on the 1363435-th line has zero coordinate or zero lengths


Warning: the feature on the 1369175-th line has zero coordinate or zero lengths


Warning: the feature on the 1375256-th line has zero coordinate or zero lengths


Warning: the feature on the 1375391-th line has zero coordinate or zero lengths


Warning: the feature on the 1376890-th line has zero coordinate or zero lengths


Warning: the feature on the 1377186-th line has zero coordinate or zero lengths


Warning: the feature on the 1380856-th line has zero coordinate or zero lengths


Warning: the feature on the 1389185-th line has zero coordinate or zero lengths


Warning: the feature on the 1390070-th line has zero coordinate or zero lengths


Warning: the feature on the 1390135-th line has zero coordinate or zero lengths


Warning: the feature on the 1393356-th line has zero coordinate or zero lengths


Warning: the feature on the 1402905-th line has zero coordinate or zero lengths


Warning: the feature on the 1408520-th line has zero coordinate or zero lengths


Warning: the feature on the 1409660-th line has zero coordinate or zero lengths


Warning: the feature on the 1413222-th line has zero coordinate or zero lengths


Warning: the feature on the 1418315-th line has zero coordinate or zero lengths


Warning: the feature on the 1423997-th line has zero coordinate or zero lengths


Warning: the feature on the 1429649-th line has zero coordinate or zero lengths


Warning: the feature on the 1456448-th line has zero coordinate or zero lengths


Warning: the feature on the 1461836-th line has zero coordinate or zero lengths


Warning: the feature on the 1461913-th line has zero coordinate or zero lengths


Warning: the feature on the 1474030-th line has zero coordinate or zero lengths


Warning: the feature on the 1474986-th line has zero coordinate or zero lengths


Warning: the feature on the 1477068-th line has zero coordinate or zero lengths


Warning: the feature on the 1480226-th line has zero coordinate or zero lengths


Warning: the feature on the 1485293-th line has zero coordinate or zero lengths


Warning: the feature on the 1504030-th line has zero coordinate or zero lengths


Warning: the feature on the 1505145-th line has zero coordinate or zero lengths


Warning: the feature on the 1515038-th line has zero coordinate or zero lengths


Warning: the feature on the 1521378-th line has zero coordinate or zero lengths


Warning: the feature on the 1538545-th line has zero coordinate or zero lengths


Warning: the feature on the 1552674-th line has zero coordinate or zero lengths


Warning: the feature on the 1561707-th line has zero coordinate or zero lengths


Warning: the feature on the 1561825-th line has zero coordinate or zero lengths


Warning: the feature on the 1564939-th line has zero coordinate or zero lengths


Warning: the feature on the 1564991-th line has zero coordinate or zero lengths


Warning: the feature on the 1573603-th line has zero coordinate or zero lengths


Warning: the feature on the 1579051-th line has zero coordinate or zero lengths


Warning: the feature on the 1579768-th line has zero coordinate or zero lengths


Warning: the feature on the 1587058-th line has zero coordinate or zero lengths


Warning: the feature on the 1587059-th line has zero coordinate or zero lengths

There are 1592247 features loaded from the annotation file.
The 1592247 features are sorted.
Number of chromosomes included in the annotation is 46

 *** caught segfault ***
address 0x6d4b8fa77010, cause 'memory not mapped'

Traceback:
 1: .C("R_readSummary_wrapper", as.integer(n), as.character(cmd),     PACKAGE = "Rsubread")
 2: featureCounts(files = "tophat_out/accepted_hits.sort.bam",     file.type = "BAM", annot = "mm10/annotation/mm10.allmrna.gtf",     isGTFAnnotationFile = TRUE, GTF.featureType = "exon", GTF.attrType = "gene_id",     useMetaFeatures = TRUE, nthreads = 1, isPairedEnd = TRUE,     checkFragLength = TRUE)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

