[M::main_mem] read 3000000 sequences (300000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (52, 43407, 11, 39) [M::mem_pestat] analyzing insert size distribution for orientation FF... [M::mem_pestat] (25, 50, 75) percentile: (29, 57, 119) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 299) [M::mem_pestat] mean and std.dev: (78.58, 69.69) [M::mem_pestat] low and high boundaries for proper pairs: (1, 389) [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (138, 170, 215) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 369) [M::mem_pestat] mean and std.dev: (178.02, 55.57) [M::mem_pestat] low and high boundaries for proper pairs: (1, 446) [M::mem_pestat] analyzing insert size distribution for orientation RF... [M::mem_pestat] (25, 50, 75) percentile: (47, 488, 1450) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4256) [M::mem_pestat] mean and std.dev: (616.90, 627.88) [M::mem_pestat] low and high boundaries for proper pairs: (1, 5659) [M::mem_pestat] analyzing insert size distribution for orientation RR... [M::mem_pestat] (25, 50, 75) percentile: (28, 49, 116) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 292) [M::mem_pestat] mean and std.dev: (65.00, 52.10) [M::mem_pestat] low and high boundaries for proper pairs: (1, 380) [M::mem_pestat] skip orientation FF [M::mem_pestat] skip orientation RF [M::mem_pestat] skip orientation RR [M::mem_process_seqs] Processed 3000000 reads in 426.582 CPU sec, 14.758 real sec [samopen] SAM header is present: 119505 sequences. [M::main_mem] read 3000000 sequences (300000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (49, 43197, 17, 56) [M::mem_pestat] analyzing insert size distribution for orientation FF... [M::mem_pestat] (25, 50, 75) percentile: (29, 66, 177) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 473) [M::mem_pestat] mean and std.dev: (90.43, 85.14) [M::mem_pestat] low and high boundaries for proper pairs: (1, 621) [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (138, 169, 214) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 366) [M::mem_pestat] mean and std.dev: (177.22, 54.89) [M::mem_pestat] low and high boundaries for proper pairs: (1, 442) [M::mem_pestat] analyzing insert size distribution for orientation RF... [M::mem_pestat] (25, 50, 75) percentile: (28, 245, 1100) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3244) [M::mem_pestat] mean and std.dev: (564.94, 852.15) [M::mem_pestat] low and high boundaries for proper pairs: (1, 4316) [M::mem_pestat] analyzing insert size distribution for orientation RR... [M::mem_pestat] (25, 50, 75) percentile: (24, 44, 152) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 408) [M::mem_pestat] mean and std.dev: (67.84, 72.30) [M::mem_pestat] low and high boundaries for proper pairs: (1, 536) [M::mem_pestat] skip orientation FF [M::mem_pestat] skip orientation RF [M::mem_pestat] skip orientation RR [M::mem_process_seqs] Processed 3000000 reads in 404.777 CPU sec, 13.859 real sec [M::main_mem] read 3000000 sequences (300000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (53, 42573, 8, 57) [M::mem_pestat] analyzing insert size distribution for orientation FF... [M::mem_pestat] (25, 50, 75) percentile: (21, 74, 162) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 444) [M::mem_pestat] mean and std.dev: (93.20, 92.48) [M::mem_pestat] low and high boundaries for proper pairs: (1, 585) [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (138, 169, 215) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 369) [M::mem_pestat] mean and std.dev: (177.61, 55.48) [M::mem_pestat] low and high boundaries for proper pairs: (1, 446) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation RR... [M::mem_pestat] (25, 50, 75) percentile: (32, 58, 135) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 341) [M::mem_pestat] mean and std.dev: (74.89, 63.94) [M::mem_pestat] low and high boundaries for proper pairs: (1, 444) [M::mem_pestat] skip orientation FF [M::mem_pestat] skip orientation RR [M::mem_process_seqs] Processed 3000000 reads in 405.874 CPU sec, 13.944 real sec [M::main_mem] read 3000000 sequences (300000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (61, 42543, 9, 46) [M::mem_pestat] analyzing insert size distribution for orientation FF... [M::mem_pestat] (25, 50, 75) percentile: (21, 45, 141) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 381) [M::mem_pestat] mean and std.dev: (76.00, 77.51) [M::mem_pestat] low and high boundaries for proper pairs: (1, 501) [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (138, 169, 214) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 366) [M::mem_pestat] mean and std.dev: (177.13, 54.81) [M::mem_pestat] low and high boundaries for proper pairs: (1, 442) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation RR... [M::mem_pestat] (25, 50, 75) percentile: (14, 54, 100) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 272) [M::mem_pestat] mean and std.dev: (55.81, 47.24) [M::mem_pestat] low and high boundaries for proper pairs: (1, 358) [M::mem_pestat] skip orientation FF [M::mem_pestat] skip orientation RR [M::mem_process_seqs] Processed 3000000 reads in 405.799 CPU sec, 13.914 real sec [M::main_mem] read 3000000 sequences (300000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (44, 42889, 19, 43) [M::mem_pestat] analyzing insert size distribution for orientation FF... [M::mem_pestat] (25, 50, 75) percentile: (28, 55, 120) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 304) [M::mem_pestat] mean and std.dev: (65.72, 58.64) [M::mem_pestat] low and high boundaries for proper pairs: (1, 396) [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (138, 170, 215) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 369) [M::mem_pestat] mean and std.dev: (177.90, 55.59) [M::mem_pestat] low and high boundaries for proper pairs: (1, 446) [M::mem_pestat] analyzing insert size distribution for orientation RF... [M::mem_pestat] (25, 50, 75) percentile: (54, 195, 3237) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9603) [M::mem_pestat] mean and std.dev: (1587.53, 2243.33) [M::mem_pestat] low and high boundaries for proper pairs: (1, 12786) [M::mem_pestat] analyzing insert size distribution for orientation RR... [M::mem_pestat] (25, 50, 75) percentile: (32, 72, 121) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 299) [M::mem_pestat] mean and std.dev: (70.75, 52.63) [M::mem_pestat] low and high boundaries for proper pairs: (1, 388) [M::mem_pestat] skip orientation FF [M::mem_pestat] skip orientation RF [M::mem_pestat] skip orientation RR [M::mem_process_seqs] Processed 3000000 reads in 410.603 CPU sec, 14.198 real sec [M::main_mem] read 3000000 sequences (300000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (51, 42712, 19, 54) [M::mem_pestat] analyzing insert size distribution for orientation FF... [M::mem_pestat] (25, 50, 75) percentile: (21, 38, 113) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 297) [M::mem_pestat] mean and std.dev: (57.57, 53.32) [M::mem_pestat] low and high boundaries for proper pairs: (1, 389) [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (139, 170, 216) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 370) [M::mem_pestat] mean and std.dev: (178.47, 55.97) [M::mem_pestat] low and high boundaries for proper pairs: (1, 447) [M::mem_pestat] analyzing insert size distribution for orientation RF... [M::mem_pestat] (25, 50, 75) percentile: (93, 255, 1079) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3051) [M::mem_pestat] mean and std.dev: (705.37, 810.82) [M::mem_pestat] low and high boundaries for proper pairs: (1, 4037) [M::mem_pestat] analyzing insert size distribution for orientation RR... [M::mem_pestat] (25, 50, 75) percentile: (29, 55, 117) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 293) [M::mem_pestat] mean and std.dev: (62.11, 48.35) [M::mem_pestat] low and high boundaries for proper pairs: (1, 381) [M::mem_pestat] skip orientation FF [M::mem_pestat] skip orientation RF [M::mem_pestat] skip orientation RR [M::mem_process_seqs] Processed 3000000 reads in 409.116 CPU sec, 14.010 real sec [M::main_mem] read 3000000 sequences (300000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (64, 42797, 9, 59) [M::mem_pestat] analyzing insert size distribution for orientation FF... [M::mem_pestat] (25, 50, 75) percentile: (27, 54, 145) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 381) [M::mem_pestat] mean and std.dev: (81.86, 83.68) [M::mem_pestat] low and high boundaries for proper pairs: (1, 499) [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (138, 170, 215) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 369) [M::mem_pestat] mean and std.dev: (177.74, 55.75) [M::mem_pestat] low and high boundaries for proper pairs: (1, 446) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation RR... [M::mem_pestat] (25, 50, 75) percentile: (22, 57, 106) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 274) [M::mem_pestat] mean and std.dev: (61.68, 49.26) [M::mem_pestat] low and high boundaries for proper pairs: (1, 358) [M::mem_pestat] skip orientation FF [M::mem_pestat] skip orientation RR [M::mem_process_seqs] Processed 3000000 reads in 409.865 CPU sec, 14.016 real sec [M::main_mem] read 3000000 sequences (300000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (55, 43008, 13, 47) [M::mem_pestat] analyzing insert size distribution for orientation FF... [M::mem_pestat] (25, 50, 75) percentile: (24, 52, 150) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 402) [M::mem_pestat] mean and std.dev: (77.54, 82.45) [M::mem_pestat] low and high boundaries for proper pairs: (1, 528) [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (139, 170, 216) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 370) [M::mem_pestat] mean and std.dev: (178.18, 55.61) [M::mem_pestat] low and high boundaries for proper pairs: (1, 447) [M::mem_pestat] analyzing insert size distribution for orientation RF... [M::mem_pestat] (25, 50, 75) percentile: (177, 365, 3811) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11079) [M::mem_pestat] mean and std.dev: (1833.54, 2078.84) [M::mem_pestat] low and high boundaries for proper pairs: (1, 14713) [M::mem_pestat] analyzing insert size distribution for orientation RR... [M::mem_pestat] (25, 50, 75) percentile: (27, 44, 106) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 264) [M::mem_pestat] mean and std.dev: (57.71, 60.13) [M::mem_pestat] low and high boundaries for proper pairs: (1, 343) [M::mem_pestat] skip orientation FF [M::mem_pestat] skip orientation RF [M::mem_pestat] skip orientation RR [M::mem_process_seqs] Processed 3000000 reads in 407.285 CPU sec, 14.095 real sec [M::main_mem] read 3000000 sequences (300000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (55, 43227, 12, 51) [M::mem_pestat] analyzing insert size distribution for orientation FF... [M::mem_pestat] (25, 50, 75) percentile: (20, 47, 100) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 260) [M::mem_pestat] mean and std.dev: (56.66, 55.04) [M::mem_pestat] low and high boundaries for proper pairs: (1, 340) [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (138, 170, 216) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 372) [M::mem_pestat] mean and std.dev: (178.25, 56.10) [M::mem_pestat] low and high boundaries for proper pairs: (1, 450) [M::mem_pestat] analyzing insert size distribution for orientation RF... [M::mem_pestat] (25, 50, 75) percentile: (284, 680, 3159) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 8909) [M::mem_pestat] mean and std.dev: (1776.58, 1937.00) [M::mem_pestat] low and high boundaries for proper pairs: (1, 11784) [M::mem_pestat] analyzing insert size distribution for orientation RR... [M::mem_pestat] (25, 50, 75) percentile: (23, 60, 128) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 338) [M::mem_pestat] mean and std.dev: (81.10, 75.99) [M::mem_pestat] low and high boundaries for proper pairs: (1, 443) [M::mem_pestat] skip orientation FF [M::mem_pestat] skip orientation RF [M::mem_pestat] skip orientation RR [M::mem_process_seqs] Processed 3000000 reads in 438.934 CPU sec, 15.066 real sec [M::main_mem] read 3000000 sequences (300000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (61, 42797, 14, 47) [M::mem_pestat] analyzing insert size distribution for orientation FF... [M::mem_pestat] (25, 50, 75) percentile: (31, 52, 184) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 490) [M::mem_pestat] mean and std.dev: (95.05, 106.78) [M::mem_pestat] low and high boundaries for proper pairs: (1, 643) [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (139, 170, 216) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 370) [M::mem_pestat] mean and std.dev: (178.28, 55.73) [M::mem_pestat] low and high boundaries for proper pairs: (1, 447) [M::mem_pestat] analyzing insert size distribution for orientation RF... [M::mem_pestat] (25, 50, 75) percentile: (43, 1021, 2609) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7741) [M::mem_pestat] mean and std.dev: (1561.36, 1651.59) [M::mem_pestat] low and high boundaries for proper pairs: (1, 10307) [M::mem_pestat] analyzing insert size distribution for orientation RR... [M::mem_pestat] (25, 50, 75) percentile: (21, 50, 94) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 240) [M::mem_pestat] mean and std.dev: (59.70, 45.59) [M::mem_pestat] low and high boundaries for proper pairs: (1, 313) [M::mem_pestat] skip orientation FF [M::mem_pestat] skip orientation RF [M::mem_pestat] skip orientation RR [M::mem_process_seqs] Processed 3000000 reads in 561.630 CPU sec, 19.834 real sec [M::main_mem] read 3000000 sequences (300000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (58, 42613, 9, 43) [M::mem_pestat] analyzing insert size distribution for orientation FF... [M::mem_pestat] (25, 50, 75) percentile: (24, 57, 134) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 354) [M::mem_pestat] mean and std.dev: (69.31, 72.11) [M::mem_pestat] low and high boundaries for proper pairs: (1, 464) [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (139, 170, 216) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 370) [M::mem_pestat] mean and std.dev: (178.14, 55.49) [M::mem_pestat] low and high boundaries for proper pairs: (1, 447) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation RR... [M::mem_pestat] (25, 50, 75) percentile: (22, 48, 95) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 241) [M::mem_pestat] mean and std.dev: (60.60, 55.15) [M::mem_pestat] low and high boundaries for proper pairs: (1, 314) [M::mem_pestat] skip orientation FF [M::mem_pestat] skip orientation RR [M::mem_process_seqs] Processed 3000000 reads in 559.815 CPU sec, 19.450 real sec [M::main_mem] read 3000000 sequences (300000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (49, 42661, 15, 51) [M::mem_pestat] analyzing insert size distribution for orientation FF... [M::mem_pestat] (25, 50, 75) percentile: (26, 67, 119) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 305) [M::mem_pestat] mean and std.dev: (77.28, 65.90) [M::mem_pestat] low and high boundaries for proper pairs: (1, 398) [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (138, 170, 216) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 372) [M::mem_pestat] mean and std.dev: (178.02, 56.04) [M::mem_pestat] low and high boundaries for proper pairs: (1, 450) [M::mem_pestat] analyzing insert size distribution for orientation RF... [M::mem_pestat] (25, 50, 75) percentile: (52, 419, 985) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2851) [M::mem_pestat] mean and std.dev: (750.13, 876.56) [M::mem_pestat] low and high boundaries for proper pairs: (1, 3784) [M::mem_pestat] analyzing insert size distribution for orientation RR... [M::mem_pestat] (25, 50, 75) percentile: (21, 55, 141) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 381) [M::mem_pestat] mean and std.dev: (84.44, 82.61) [M::mem_pestat] low and high boundaries for proper pairs: (1, 501) [M::mem_pestat] skip orientation FF [M::mem_pestat] skip orientation RF [M::mem_pestat] skip orientation RR [M::mem_process_seqs] Processed 3000000 reads in 561.585 CPU sec, 23.268 real sec [M::main_mem] read 3000000 sequences (300000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (53, 42660, 28, 48) [M::mem_pestat] analyzing insert size distribution for orientation FF... [M::mem_pestat] (25, 50, 75) percentile: (20, 53, 152) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 416) [M::mem_pestat] mean and std.dev: (80.92, 89.26) [M::mem_pestat] low and high boundaries for proper pairs: (1, 548) [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (138, 169, 216) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 372) [M::mem_pestat] mean and std.dev: (178.11, 56.18) [M::mem_pestat] low and high boundaries for proper pairs: (1, 450) [M::mem_pestat] analyzing insert size distribution for orientation RF... [M::mem_pestat] (25, 50, 75) percentile: (224, 995, 2334) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6554) [M::mem_pestat] mean and std.dev: (1408.71, 1329.66) [M::mem_pestat] low and high boundaries for proper pairs: (1, 8664) [M::mem_pestat] analyzing insert size distribution for orientation RR... [M::mem_pestat] (25, 50, 75) percentile: (25, 51, 191) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 523) [M::mem_pestat] mean and std.dev: (87.00, 95.56) [M::mem_pestat] low and high boundaries for proper pairs: (1, 689) [M::mem_pestat] skip orientation FF [M::mem_pestat] skip orientation RF [M::mem_pestat] skip orientation RR [M::mem_process_seqs] Processed 3000000 reads in 559.719 CPU sec, 24.352 real sec [M::main_mem] read 3000000 sequences (300000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (54, 42416, 17, 48) [M::mem_pestat] analyzing insert size distribution for orientation FF... [M::mem_pestat] (25, 50, 75) percentile: (28, 59, 124) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 316) [M::mem_pestat] mean and std.dev: (70.98, 61.09) [M::mem_pestat] low and high boundaries for proper pairs: (1, 412) [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (138, 169, 215) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 369) [M::mem_pestat] mean and std.dev: (177.79, 55.82) [M::mem_pestat] low and high boundaries for proper pairs: (1, 446) [M::mem_pestat] analyzing insert size distribution for orientation RF... [M::mem_pestat] (25, 50, 75) percentile: (78, 143, 1208) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3468) [M::mem_pestat] mean and std.dev: (575.25, 785.02) [M::mem_pestat] low and high boundaries for proper pairs: (1, 4598) [M::mem_pestat] analyzing insert size distribution for orientation RR... [M::mem_pestat] (25, 50, 75) percentile: (22, 55, 91) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 229) [M::mem_pestat] mean and std.dev: (57.07, 48.51) [M::mem_pestat] low and high boundaries for proper pairs: (1, 298) [M::mem_pestat] skip orientation FF [M::mem_pestat] skip orientation RF [M::mem_pestat] skip orientation RR [M::mem_process_seqs] Processed 3000000 reads in 563.365 CPU sec, 25.550 real sec [M::main_mem] read 3000000 sequences (300000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (50, 42417, 10, 56) [M::mem_pestat] analyzing insert size distribution for orientation FF... [M::mem_pestat] (25, 50, 75) percentile: (27, 66, 96) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 234) [M::mem_pestat] mean and std.dev: (63.61, 44.29) [M::mem_pestat] low and high boundaries for proper pairs: (1, 303) [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (138, 169, 214) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 366) [M::mem_pestat] mean and std.dev: (177.08, 55.17) [M::mem_pestat] low and high boundaries for proper pairs: (1, 442) [M::mem_pestat] analyzing insert size distribution for orientation RF... [M::mem_pestat] (25, 50, 75) percentile: (225, 839, 1418) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3804) [M::mem_pestat] mean and std.dev: (604.00, 494.46) [M::mem_pestat] low and high boundaries for proper pairs: (1, 4997) [M::mem_pestat] analyzing insert size distribution for orientation RR... [M::mem_pestat] (25, 50, 75) percentile: (23, 60, 104) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 266) [M::mem_pestat] mean and std.dev: (63.85, 55.15) [M::mem_pestat] low and high boundaries for proper pairs: (1, 347) [M::mem_pestat] skip orientation FF [M::mem_pestat] skip orientation RF [M::mem_pestat] skip orientation RR [M::mem_process_seqs] Processed 3000000 reads in 554.504 CPU sec, 22.626 real sec [M::main_mem] read 3000000 sequences (300000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (51, 42923, 13, 57) [M::mem_pestat] analyzing insert size distribution for orientation FF... [M::mem_pestat] (25, 50, 75) percentile: (17, 52, 100) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 266) [M::mem_pestat] mean and std.dev: (58.17, 51.08) [M::mem_pestat] low and high boundaries for proper pairs: (1, 349) [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (138, 170, 215) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 369) [M::mem_pestat] mean and std.dev: (177.85, 55.65) [M::mem_pestat] low and high boundaries for proper pairs: (1, 446) [M::mem_pestat] analyzing insert size distribution for orientation RF... [M::mem_pestat] (25, 50, 75) percentile: (147, 271, 709) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1833) [M::mem_pestat] mean and std.dev: (296.45, 211.38) [M::mem_pestat] low and high boundaries for proper pairs: (1, 2395) [M::mem_pestat] analyzing insert size distribution for orientation RR... [M::mem_pestat] (25, 50, 75) percentile: (23, 48, 151) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 407) [M::mem_pestat] mean and std.dev: (83.77, 92.84) [M::mem_pestat] low and high boundaries for proper pairs: (1, 535) [M::mem_pestat] skip orientation FF [M::mem_pestat] skip orientation RF [M::mem_pestat] skip orientation RR [M::mem_process_seqs] Processed 3000000 reads in 500.853 CPU sec, 17.281 real sec [M::main_mem] read 3000000 sequences (300000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (68, 42763, 17, 44) [M::mem_pestat] analyzing insert size distribution for orientation FF... [M::mem_pestat] (25, 50, 75) percentile: (19, 58, 140) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 382) [M::mem_pestat] mean and std.dev: (86.10, 82.81) [M::mem_pestat] low and high boundaries for proper pairs: (1, 503) [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (139, 170, 216) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 370) [M::mem_pestat] mean and std.dev: (178.34, 56.11) [M::mem_pestat] low and high boundaries for proper pairs: (1, 447) [M::mem_pestat] analyzing insert size distribution for orientation RF... [M::mem_pestat] (25, 50, 75) percentile: (56, 477, 2704) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 8000) [M::mem_pestat] mean and std.dev: (1610.65, 2489.78) [M::mem_pestat] low and high boundaries for proper pairs: (1, 10648) [M::mem_pestat] analyzing insert size distribution for orientation RR... [M::mem_pestat] (25, 50, 75) percentile: (10, 34, 91) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 253) [M::mem_pestat] mean and std.dev: (52.57, 62.27) [M::mem_pestat] low and high boundaries for proper pairs: (1, 334) [M::mem_pestat] skip orientation FF [M::mem_pestat] skip orientation RF [M::mem_pestat] skip orientation RR [M::mem_process_seqs] Processed 3000000 reads in 452.684 CPU sec, 15.430 real sec [M::main_mem] read 3000000 sequences (300000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (58, 42588, 11, 43) [M::mem_pestat] analyzing insert size distribution for orientation FF... [M::mem_pestat] (25, 50, 75) percentile: (19, 83, 202) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 568) [M::mem_pestat] mean and std.dev: (115.80, 132.27) [M::mem_pestat] low and high boundaries for proper pairs: (1, 751) [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (139, 170, 215) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 367) [M::mem_pestat] mean and std.dev: (178.05, 55.41) [M::mem_pestat] low and high boundaries for proper pairs: (1, 443) [M::mem_pestat] analyzing insert size distribution for orientation RF... [M::mem_pestat] (25, 50, 75) percentile: (24, 72, 3612) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10788) [M::mem_pestat] mean and std.dev: (1803.82, 2592.01) [M::mem_pestat] low and high boundaries for proper pairs: (1, 14376) [M::mem_pestat] analyzing insert size distribution for orientation RR... [M::mem_pestat] (25, 50, 75) percentile: (28, 65, 124) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 316) [M::mem_pestat] mean and std.dev: (73.65, 62.94) [M::mem_pestat] low and high boundaries for proper pairs: (1, 412) [M::mem_pestat] skip orientation FF [M::mem_pestat] skip orientation RF [M::mem_pestat] skip orientation RR [M::mem_process_seqs] Processed 3000000 reads in 468.366 CPU sec, 16.078 real sec [M::main_mem] read 3000000 sequences (300000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (56, 42728, 15, 42) [M::mem_pestat] analyzing insert size distribution for orientation FF... [M::mem_pestat] (25, 50, 75) percentile: (19, 49, 159) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 439) [M::mem_pestat] mean and std.dev: (77.00, 81.17) [M::mem_pestat] low and high boundaries for proper pairs: (1, 579) [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (138, 170, 215) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 369) [M::mem_pestat] mean and std.dev: (178.08, 55.61) [M::mem_pestat] low and high boundaries for proper pairs: (1, 446) [M::mem_pestat] analyzing insert size distribution for orientation RF... [M::mem_pestat] (25, 50, 75) percentile: (33, 86, 500) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1434) [M::mem_pestat] mean and std.dev: (223.79, 297.87) [M::mem_pestat] low and high boundaries for proper pairs: (1, 1901) [M::mem_pestat] analyzing insert size distribution for orientation RR... [M::mem_pestat] (25, 50, 75) percentile: (16, 46, 103) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 277) [M::mem_pestat] mean and std.dev: (62.21, 60.02) [M::mem_pestat] low and high boundaries for proper pairs: (1, 364) [M::mem_pestat] skip orientation FF [M::mem_pestat] skip orientation RF [M::mem_pestat] skip orientation RR [M::mem_process_seqs] Processed 3000000 reads in 487.827 CPU sec, 16.833 real sec [M::main_mem] read 3000000 sequences (300000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (62, 42724, 23, 48) [M::mem_pestat] analyzing insert size distribution for orientation FF... [M::mem_pestat] (25, 50, 75) percentile: (21, 65, 133) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 357) [M::mem_pestat] mean and std.dev: (83.83, 81.10) [M::mem_pestat] low and high boundaries for proper pairs: (1, 469) [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (139, 170, 216) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 370) [M::mem_pestat] mean and std.dev: (178.11, 55.78) [M::mem_pestat] low and high boundaries for proper pairs: (1, 447) [M::mem_pestat] analyzing insert size distribution for orientation RF... [M::mem_pestat] (25, 50, 75) percentile: (144, 770, 2212) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6348) [M::mem_pestat] mean and std.dev: (936.00, 1035.58) [M::mem_pestat] low and high boundaries for proper pairs: (1, 8416) [M::mem_pestat] analyzing insert size distribution for orientation RR... [M::mem_pestat] (25, 50, 75) percentile: (25, 48, 122) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 316) [M::mem_pestat] mean and std.dev: (55.95, 44.54) [M::mem_pestat] low and high boundaries for proper pairs: (1, 413) [M::mem_pestat] skip orientation FF [M::mem_pestat] skip orientation RF [M::mem_pestat] skip orientation RR [M::mem_process_seqs] Processed 3000000 reads in 410.736 CPU sec, 14.169 real sec [M::main_mem] read 3000000 sequences (300000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (65, 42896, 15, 43) [M::mem_pestat] analyzing insert size distribution for orientation FF... [M::mem_pestat] (25, 50, 75) percentile: (19, 43, 154) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 424) [M::mem_pestat] mean and std.dev: (71.09, 83.01) [M::mem_pestat] low and high boundaries for proper pairs: (1, 559) [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (139, 170, 216) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 370) [M::mem_pestat] mean and std.dev: (178.43, 55.87) [M::mem_pestat] low and high boundaries for proper pairs: (1, 447) [M::mem_pestat] analyzing insert size distribution for orientation RF... [M::mem_pestat] (25, 50, 75) percentile: (65, 214, 872) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2486) [M::mem_pestat] mean and std.dev: (436.00, 611.67) [M::mem_pestat] low and high boundaries for proper pairs: (1, 3293) [M::mem_pestat] analyzing insert size distribution for orientation RR... [M::mem_pestat] (25, 50, 75) percentile: (29, 44, 81) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 185) [M::mem_pestat] mean and std.dev: (48.66, 32.50) [M::mem_pestat] low and high boundaries for proper pairs: (1, 237) [M::mem_pestat] skip orientation FF [M::mem_pestat] skip orientation RF [M::mem_pestat] skip orientation RR [M::mem_process_seqs] Processed 3000000 reads in 446.039 CPU sec, 15.200 real sec [M::main_mem] read 3000000 sequences (300000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (79, 42473, 16, 44) [M::mem_pestat] analyzing insert size distribution for orientation FF... [M::mem_pestat] (25, 50, 75) percentile: (19, 43, 97) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 253) [M::mem_pestat] mean and std.dev: (53.59, 51.29) [M::mem_pestat] low and high boundaries for proper pairs: (1, 331) [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (138, 170, 215) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 369) [M::mem_pestat] mean and std.dev: (177.65, 55.38) [M::mem_pestat] low and high boundaries for proper pairs: (1, 446) [M::mem_pestat] analyzing insert size distribution for orientation RF... [M::mem_pestat] (25, 50, 75) percentile: (71, 354, 2282) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6704) [M::mem_pestat] mean and std.dev: (1129.06, 1462.72) [M::mem_pestat] low and high boundaries for proper pairs: (1, 8915) [M::mem_pestat] analyzing insert size distribution for orientation RR... [M::mem_pestat] (25, 50, 75) percentile: (23, 41, 103) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 263) [M::mem_pestat] mean and std.dev: (53.05, 42.21) [M::mem_pestat] low and high boundaries for proper pairs: (1, 343) [M::mem_pestat] skip orientation FF [M::mem_pestat] skip orientation RF [M::mem_pestat] skip orientation RR [M::mem_process_seqs] Processed 3000000 reads in 422.669 CPU sec, 14.493 real sec [M::main_mem] read 3000000 sequences (300000000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (46, 42687, 13, 55) [M::mem_pestat] analyzing insert size distribution for orientation FF... [M::mem_pestat] (25, 50, 75) percentile: (30, 80, 151) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 393) [M::mem_pestat] mean and std.dev: (91.00, 85.06) [M::mem_pestat] low and high boundaries for proper pairs: (1, 514) [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (138, 169, 215) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 369) [M::mem_pestat] mean and std.dev: (177.65, 55.52) [M::mem_pestat] low and high boundaries for proper pairs: (1, 446) [M::mem_pestat] analyzing insert size distribution for orientation RF... [M::mem_pestat] (25, 50, 75) percentile: (68, 286, 2072) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6080) [M::mem_pestat] mean and std.dev: (1226.46, 1539.76) [M::mem_pestat] low and high boundaries for proper pairs: (1, 8084) [M::mem_pestat] analyzing insert size distribution for orientation RR... [M::mem_pestat] (25, 50, 75) percentile: (20, 37, 103) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 269) [M::mem_pestat] mean and std.dev: (58.35, 56.56) [M::mem_pestat] low and high boundaries for proper pairs: (1, 352) [M::mem_pestat] skip orientation FF [M::mem_pestat] skip orientation RF [M::mem_pestat] skip orientation RR [M::mem_process_seqs] Processed 3000000 reads in 479.356 CPU sec, 16.665 real sec [M::main_mem] read 503464 sequences (50346400 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 7169, 0, 5) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (138, 171, 217) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 375) [M::mem_pestat] mean and std.dev: (178.70, 57.12) [M::mem_pestat] low and high boundaries for proper pairs: (1, 454) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 503464 reads in 82.192 CPU sec, 3.120 real sec [main] Version: 0.7.8-r455 [main] CMD: /MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/TRAIL_V5/bwa mem -t 30 /MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/AllRef.fa /MGMSTAR1/SHARED/ANALYSIS/NGS_P2207/R341_Transcriptome/RAW_DATA/ALL/FINAL/2207.LIB14116_New_CAGATC_S12_T_R1.fastq.gz /MGMSTAR1/SHARED/ANALYSIS/NGS_P2207/R341_Transcriptome/RAW_DATA/ALL/FINAL/2207.LIB14116_New_CAGATC_S12_T_R2.fastq.gz [main] Real time: 1438.714 sec; CPU: 11008.804 sec # License expires in 14.0 days. # novoalign (V3.04.01 - Build Jan 13 2016 @ 10:07:29) - A short read aligner with qualities. # (C) 2008-2015 Novocraft Technologies Sdn Bhd. # License file: /MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/TRAIL_V5/novoalign.lic # Licensed to K Thangaraj@CCMB # novoalign -r A 1 -n 30 -d /MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/AllRef.ndx -f /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.main.bwa.unmapped_1.fastq /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.main.bwa.unmapped_2.fastq -o SAM # Starting at Tue Jun 21 14:37:28 2016 # Interpreting input files as Sanger FASTQ. # Index Build Version: 3.4 # Hash length: 14 # Step size: 2 # Paired Reads: 1364385 # Proper Pairs: 318517 (23.3%) # Read Sequences: 2728770 # Unique Alignment: 224108 ( 8.2%) # Multi Mapped: 1068088 (39.1%) # No Mapping Found: 1334328 (48.9%) # QC Failures... # Homopolymer Filter: 732 ( 0.0%) # Read Length: 101514 ( 3.7%) # Elapsed Time: 598.564 (secs.) # CPU Time: 299.53 (min.) # Fragment Length Distribution # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # Mean 528, Std Dev 192.9 # Done at Tue Jun 21 14:50:44 2016 [samopen] SAM header is present: 119505 sequences. Traceback (most recent call last): File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/bin/mp_blat.py", line 152, in mp_blat(args.reference, args.fasta, args.output, args.process, args.tmp_path, args.blat_bin, args.blat_opt) File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/bin/mp_blat.py", line 23, in mp_blat print >> sys.stderr, "Start to split the input into {} part ... ".format(num_of_process) ValueError: zero length field name in format cat: /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.rG.psl: No such file or directory cat: /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.rG.psl: No such file or directory PslChimeraFilter v0.4 Traceback (most recent call last): File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/bin/mp_blat.py", line 152, in mp_blat(args.reference, args.fasta, args.output, args.process, args.tmp_path, args.blat_bin, args.blat_opt) File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/bin/mp_blat.py", line 23, in mp_blat print >> sys.stderr, "Start to split the input into {} part ... ".format(num_of_process) ValueError: zero length field name in format Traceback (most recent call last): File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/bin/mp_blat.py", line 152, in mp_blat(args.reference, args.fasta, args.output, args.process, args.tmp_path, args.blat_bin, args.blat_opt) File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/bin/mp_blat.py", line 23, in mp_blat print >> sys.stderr, "Start to split the input into {} part ... ".format(num_of_process) ValueError: zero length field name in format Traceback (most recent call last): File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/bin/mp_blat.py", line 152, in mp_blat(args.reference, args.fasta, args.output, args.process, args.tmp_path, args.blat_bin, args.blat_opt) File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/bin/mp_blat.py", line 23, in mp_blat print >> sys.stderr, "Start to split the input into {} part ... ".format(num_of_process) ValueError: zero length field name in format cat: /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.coding.2.psl: No such file or directory cat: /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.lncRNA.2.psl: No such file or directory cat: /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.chrM.2.psl: No such file or directory JunctionSite2BED v0.3 Reading annotations on chr1. Reading annotations on chr2. Reading annotations on chr3. Reading annotations on chr4. Reading annotations on chr5. Reading annotations on chr6. Reading annotations on chr7. Reading annotations on chr8. Reading annotations on chr9. Reading annotations on chr10. Reading annotations on chr11. Reading annotations on chr12. Reading annotations on chr13. Reading annotations on chr14. Reading annotations on chr15. Reading annotations on chr16. Reading annotations on chr17. Reading annotations on chr18. Reading annotations on chr19. Reading annotations on chr20. Reading annotations on chr21. Reading annotations on chr22. Reading annotations on chrX. Reading annotations on chrY. Reading annotations on chrM. Read 57820 genes, 196520 transcripts and 1196293 exons from the gtf file. Error: The requested bed file (/MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.preJS.bed) could not be opened. Exiting! # novoindex (3.4) - Universal k-mer index constructor. # (C) 2008 - 2011 NovoCraft Technologies Sdn Bhd # novoindex /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.JS.ndx /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.JS.fa # Creating 72 indexing threads. # Building with 6-mer and step of 1 bp. # novoindex construction dT = 0.0s # Index memory size 0.000Gbyte. # Done. # License expires in 14.0 days. # novoalign (V3.04.01 - Build Jan 13 2016 @ 10:07:29) - A short read aligner with qualities. # (C) 2008-2015 Novocraft Technologies Sdn Bhd. # License file: /MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/TRAIL_V5/novoalign.lic # Licensed to K Thangaraj@CCMB # novoalign -r A 1 -g 99 -x 99 -d /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.JS.ndx -f /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.main.unmapped_1.fastq -o SAM # Starting at Tue Jun 21 14:52:44 2016 # Interpreting input files as Sanger FASTQ. Error: /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.JS.ndx does not appear to be a valid novoindex. Code 9 # License expires in 14.0 days. # novoalign (V3.04.01 - Build Jan 13 2016 @ 10:07:29) - A short read aligner with qualities. # (C) 2008-2015 Novocraft Technologies Sdn Bhd. # License file: /MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/TRAIL_V5/novoalign.lic # Licensed to K Thangaraj@CCMB # novoalign -r A 1 -g 99 -x 99 -d /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.JS.ndx -f /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.main.unmapped_2.fastq -o SAM # Starting at Tue Jun 21 14:52:44 2016 # Interpreting input files as Sanger FASTQ. Error: /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.JS.ndx does not appear to be a valid novoindex. Code 9 Traceback (most recent call last): File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/bin/mp_blat.py", line 152, in mp_blat(args.reference, args.fasta, args.output, args.process, args.tmp_path, args.blat_bin, args.blat_opt) File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/bin/mp_blat.py", line 23, in mp_blat print >> sys.stderr, "Start to split the input into {} part ... ".format(num_of_process) ValueError: zero length field name in format cat: /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.JS.GRCh37.psl: No such file or directory Traceback (most recent call last): File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/bin/mp_blat.py", line 152, in mp_blat(args.reference, args.fasta, args.output, args.process, args.tmp_path, args.blat_bin, args.blat_opt) File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/bin/mp_blat.py", line 23, in mp_blat print >> sys.stderr, "Start to split the input into {} part ... ".format(num_of_process) ValueError: zero length field name in format cat: /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.2.info.GRCh37.psl: No such file or directory PslChimeraFilter v0.4 JunctionSite2BED v0.3 Reading annotations on chr1. Reading annotations on chr2. Reading annotations on chr3. Reading annotations on chr4. Reading annotations on chr5. Reading annotations on chr6. Reading annotations on chr7. Reading annotations on chr8. Reading annotations on chr9. Reading annotations on chr10. Reading annotations on chr11. Reading annotations on chr12. Reading annotations on chr13. Reading annotations on chr14. Reading annotations on chr15. Reading annotations on chr16. Reading annotations on chr17. Reading annotations on chr18. Reading annotations on chr19. Reading annotations on chr20. Reading annotations on chr21. Reading annotations on chr22. Reading annotations on chrX. Reading annotations on chrY. Reading annotations on chrM. Read 57820 genes, 196520 transcripts and 1196293 exons from the gtf file. Error: The requested bed file (/MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.PreJS2.bed) could not be opened. Exiting! # novoindex (3.4) - Universal k-mer index constructor. # (C) 2008 - 2011 NovoCraft Technologies Sdn Bhd # novoindex /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.JS2.ndx /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.JS2.fa # Creating 72 indexing threads. # Building with 6-mer and step of 1 bp. # novoindex construction dT = 0.0s # Index memory size 0.000Gbyte. # Done. # License expires in 14.0 days. # novoalign (V3.04.01 - Build Jan 13 2016 @ 10:07:29) - A short read aligner with qualities. # (C) 2008-2015 Novocraft Technologies Sdn Bhd. # License file: /MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/TRAIL_V5/novoalign.lic # Licensed to K Thangaraj@CCMB # novoalign -r A 1 -t 0,1 -d /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.JS2.ndx -f /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.main.unmapped_1.fastq /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.main.unmapped_2.fastq --3Prime -o SAM # Starting at Tue Jun 21 14:53:02 2016 # Interpreting input files as Sanger FASTQ. Error: /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.JS2.ndx does not appear to be a valid novoindex. Code 9 Traceback (most recent call last): File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/bin/mp_blat.py", line 152, in mp_blat(args.reference, args.fasta, args.output, args.process, args.tmp_path, args.blat_bin, args.blat_opt) File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/bin/mp_blat.py", line 23, in mp_blat print >> sys.stderr, "Start to split the input into {} part ... ".format(num_of_process) ValueError: zero length field name in format Traceback (most recent call last): File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/bin/mp_blat.py", line 152, in mp_blat(args.reference, args.fasta, args.output, args.process, args.tmp_path, args.blat_bin, args.blat_opt) File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/bin/mp_blat.py", line 23, in mp_blat print >> sys.stderr, "Start to split the input into {} part ... ".format(num_of_process) ValueError: zero length field name in format Traceback (most recent call last): File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/bin/mp_blat.py", line 152, in mp_blat(args.reference, args.fasta, args.output, args.process, args.tmp_path, args.blat_bin, args.blat_opt) File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/bin/mp_blat.py", line 23, in mp_blat print >> sys.stderr, "Start to split the input into {} part ... ".format(num_of_process) ValueError: zero length field name in format Traceback (most recent call last): File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/bin/mp_blat.py", line 152, in mp_blat(args.reference, args.fasta, args.output, args.process, args.tmp_path, args.blat_bin, args.blat_opt) File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/bin/mp_blat.py", line 23, in mp_blat print >> sys.stderr, "Start to split the input into {} part ... ".format(num_of_process) ValueError: zero length field name in format cat: /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.rG.um3.psl: No such file or directory cat: /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.coding.um3.psl: No such file or directory cat: /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.lncRNA.um3.psl: No such file or directory cat: /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.chrM.um3.psl: No such file or directory Traceback (most recent call last): File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/bin/Add_read_count.py", line 118, in add_read_count(args.result_tmp_file, args.result_sam_file, args.output, args.JSParser_bin) File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/bin/Add_read_count.py", line 13, in add_read_count all_junc_read_with_ref = get_junc_read(result_sam_data, JSParser_bin) File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/bin/Add_read_count.py", line 66, in get_junc_read junc_read_data = get_read_with_ref(junc_read_sam_data) File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/bin/Add_read_count.py", line 46, in get_read_with_ref ref_id = re.sub("\.[0-9]*$", "", line[2]) IndexError: list index out of range Traceback (most recent call last): File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/bin/get_gene_name.py", line 91, in add_gene_name(args.result_tmp_file, args.gene_anno, args.output) File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/bin/get_gene_name.py", line 8, in add_gene_name result_tmp_data = read_TSV(result_tmp_file) File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/bin/get_gene_name.py", line 64, in read_TSV with open(tsv_file) as data_reader: IOError: [Errno 2] No such file or directory: '/MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.result.tmp2' Traceback (most recent call last): File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/NCLscan.py", line 448, in NCL_Scan4(config, datasets_list, args.project_name, args.output_dir) File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/NCLscan.py", line 255, in NCL_Scan4 final_tmp = read_TSV("{prefix}.result.tmp3".format(**config_options)) File "/MGMSTAR1/SHARED/RESOURCES/CODE/TRANSCRIPTOME/NCLScan/NCLscan-master/V1.6/NCLscan-1.6/NCLscan.py", line 279, in read_TSV with open(tsv_file) as data_reader: IOError: [Errno 2] No such file or directory: '/MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.result.tmp3'