RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.LdCGHd/RM_8966.SunJan141621032024 Search Engine = rmblast 2.13.0+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1705278063 Database = /dev/shm/rModeler.LdCGHd/GCA_034619465.1_bLepDis1.hap2 - Sequences = 278 - Bases = 1332047658 - N50 = 83838036 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 204708959-219330182 | [ 1 ] 190087736-204708958 | [ ] 175466514-190087736 | [ ] 160845291-175466513 | [ ] 146224069-160845291 | [ ] 131602846-146224068 | [ ] 116981624-131602846 | [ 1 ] 102360401-116981623 | [ ] 87739179-102360401 | [ 1 ] 73117956-87739178 | [ 3 ] 58496734-73117956 | [ 3 ] 43875511-58496733 | [ 1 ] 29254289-43875511 | [ ] 14633066-29254288 |* [ 10 ] 11844-14633066 |************************************************** [ 258 ] Storage Throughput = excellent ( 1191.69 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40005369 bp ( 40003969 non ambiguous ) - Num Contigs Represented = 90 - Sequence extraction : 00:01:43 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:10 (hh:mm:ss) Elapsed Time Round Time: 00:36:59 (hh:mm:ss) Elapsed Time : 87 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1883 repeats masked totaling 915370 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10025467 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 10025067 bp After Masking: 8366919 bp Masked: 16.54 % -- Input Database Coverage: 10025467 bp out of 1332047658 bp ( 0.75 % ) Sampling Time: 00:03:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:13:24 (hh:mm:ss) Elapsed Time, 805 HSPs Collected Number of families returned by RECON: 255 Round Time: 00:16:42 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5838 repeats masked totaling 2397794 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30019822 bp Num Contigs Represented = 75 Non ambiguous bp: Initial: 30018822 bp After Masking: 25451731 bp Masked: 15.21 % -- Input Database Coverage: 40045289 bp out of 1332047658 bp ( 3.01 % ) Sampling Time: 00:09:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:40:52 (hh:mm:ss) Elapsed Time, 6363 HSPs Collected Number of families returned by RECON: 1269 Round Time: 00:50:54 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17561 repeats masked totaling 7088918 bp(s). - TE Masking time 00:01:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90036217 bp Num Contigs Represented = 129 Non ambiguous bp: Initial: 90032417 bp After Masking: 76866075 bp Masked: 14.62 % -- Input Database Coverage: 130081506 bp out of 1332047658 bp ( 9.77 % ) Sampling Time: 00:25:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2557191 Comparison Time: 05:43:14 (hh:mm:ss) Elapsed Time, 47846 HSPs Collected Number of families returned by RECON: 7639 Round Time: 06:23:27 (hh:mm:ss) Elapsed Time : 65 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:57:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 63677 repeats masked totaling 26587819 bp(s). - TE Masking time 00:05:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270016506 bp Num Contigs Represented = 187 Non ambiguous bp: Initial: 270005763 bp After Masking: 225935305 bp Masked: 16.32 % -- Input Database Coverage: 400098012 bp out of 1332047658 bp ( 30.04 % ) Sampling Time: 01:16:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22987590 Comparison Time: 37:07:56 (hh:mm:ss) Elapsed Time, 176279 HSPs Collected Number of families returned by RECON: 48510 Round Time: 39:07:06 (hh:mm:ss) Elapsed Time : 217 families discovered. RepeatScout/RECON discovery complete: 381 families found Classification Time: 00:47:59 (hh:mm:ss) Elapsed Time Program Time: 48:03:07 (hh:mm:ss) Elapsed Time