RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.W96mqG/RM_3210702.ThuMar282044312024 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: 1711683870 Database = /dev/shm/rModeler.W96mqG/GCA_963924515.1_mVesMur1.1 - Sequences = 178 - Bases = 1925577803 - N50 = 196849945 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 204409008-219009580 | [ 1 ] 189808436-204409008 | [ 3 ] 175207864-189808436 | [ 1 ] 160607292-175207864 | [ 1 ] 146006720-160607292 | [ ] 131406148-146006720 | [ ] 116805576-131406148 | [ ] 102205004-116805576 | [ 1 ] 87604432-102205004 | [ ] 73003860-87604432 | [ 2 ] 58403288-73003860 | [ 1 ] 43802716-58403288 |* [ 5 ] 29202144-43802716 | [ 1 ] 14601572-29202144 | [ 1 ] 1000-14601572 |************************************************** [ 161 ] Storage Throughput = excellent ( 1353.55 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40009165 bp ( 40004165 non ambiguous ) - Num Contigs Represented = 45 - Sequence extraction : 00:02:48 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:11 (hh:mm:ss) Elapsed Time Round Time: 00:25:41 (hh:mm:ss) Elapsed Time : 317 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14583 repeats masked totaling 2650380 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001781 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10000181 bp After Masking: 6947475 bp Masked: 30.53 % -- Input Database Coverage: 10001781 bp out of 1925577803 bp ( 0.52 % ) Sampling Time: 00:01:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:43 (hh:mm:ss) Elapsed Time, 5761 HSPs Collected Number of families returned by RECON: 777 Round Time: 00:07:24 (hh:mm:ss) Elapsed Time : 19 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46834 repeats masked totaling 8401044 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30007304 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 30003904 bp After Masking: 20439830 bp Masked: 31.88 % -- Input Database Coverage: 40009085 bp out of 1925577803 bp ( 2.08 % ) Sampling Time: 00:04:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:27:47 (hh:mm:ss) Elapsed Time, 22971 HSPs Collected Number of families returned by RECON: 2146 Round Time: 00:33:23 (hh:mm:ss) Elapsed Time : 57 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 151759 repeats masked totaling 26894550 bp(s). - TE Masking time 00:01:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90026959 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 90018359 bp After Masking: 60388736 bp Masked: 32.92 % -- Input Database Coverage: 130036044 bp out of 1925577803 bp ( 6.75 % ) Sampling Time: 00:12:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 02:57:26 (hh:mm:ss) Elapsed Time, 143148 HSPs Collected Number of families returned by RECON: 7926 Round Time: 03:13:06 (hh:mm:ss) Elapsed Time : 205 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:19:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 494961 repeats masked totaling 89373201 bp(s). - TE Masking time 00:05:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270053089 bp Num Contigs Represented = 92 Non ambiguous bp: Initial: 270025889 bp After Masking: 172578218 bp Masked: 36.09 % -- Input Database Coverage: 400089133 bp out of 1925577803 bp ( 20.78 % ) Sampling Time: 00:40:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22852180 Comparison Time: 23:16:04 (hh:mm:ss) Elapsed Time, 943601 HSPs Collected Number of families returned by RECON: 31882 Round Time: 24:24:12 (hh:mm:ss) Elapsed Time : 461 families discovered. RepeatScout/RECON discovery complete: 1059 families found Classification Time: 00:41:15 (hh:mm:ss) Elapsed Time Program Time: 29:25:01 (hh:mm:ss) Elapsed Time