RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.PHeqKq/RM_15007.MonJun241450402024 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: 1719265839 Database = /dev/shm/rModeler.PHeqKq/GCF_027409185.1_mCynVol1.pri - Sequences = 130 - Bases = 2814418120 - N50 = 167399654 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 284175951-304471933 | [ 1 ] 263879969-284175950 | [ ] 243583988-263879969 | [ ] 223288006-243583987 | [ 1 ] 202992025-223288006 | [ ] 182696043-202992024 | [ 1 ] 162400061-182696042 |** [ 5 ] 142104080-162400061 | [ 2 ] 121808098-142104079 | [ 2 ] 101512117-121808098 |* [ 3 ] 81216135-101512116 | [ 1 ] 60920153-81216134 | [ 1 ] 40624172-60920153 | [ 1 ] 20328190-40624171 | [ ] 32209-20328190 |************************************************* [ 112 ] Storage Throughput = excellent ( 1027.87 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40030172 bp ( 40029472 non ambiguous ) - Num Contigs Represented = 41 - Sequence extraction : 00:03:25 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:07 (hh:mm:ss) Elapsed Time Round Time: 00:40:15 (hh:mm:ss) Elapsed Time : 290 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10573 repeats masked totaling 2824849 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000699 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10000499 bp After Masking: 6757145 bp Masked: 32.43 % -- Input Database Coverage: 10000699 bp out of 2814418120 bp ( 0.36 % ) Sampling Time: 00:01:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:11 (hh:mm:ss) Elapsed Time, 7387 HSPs Collected Number of families returned by RECON: 816 Round Time: 00:07:15 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33417 repeats masked totaling 8415378 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30029393 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 30028893 bp After Masking: 20495158 bp Masked: 31.75 % -- Input Database Coverage: 40030092 bp out of 2814418120 bp ( 1.42 % ) Sampling Time: 00:06:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:28:08 (hh:mm:ss) Elapsed Time, 29854 HSPs Collected Number of families returned by RECON: 2771 Round Time: 00:35:33 (hh:mm:ss) Elapsed Time : 67 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 111251 repeats masked totaling 29011306 bp(s). - TE Masking time 00:01:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90009518 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 90008418 bp After Masking: 56288053 bp Masked: 37.46 % -- Input Database Coverage: 130039610 bp out of 2814418120 bp ( 4.62 % ) Sampling Time: 00:20:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 03:04:18 (hh:mm:ss) Elapsed Time, 133906 HSPs Collected Number of families returned by RECON: 9480 Round Time: 03:31:06 (hh:mm:ss) Elapsed Time : 202 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:22:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 378602 repeats masked totaling 96190014 bp(s). - TE Masking time 00:07:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270004888 bp Num Contigs Represented = 101 Non ambiguous bp: Initial: 270002188 bp After Masking: 162132322 bp Masked: 39.95 % -- Input Database Coverage: 400044498 bp out of 2814418120 bp ( 14.21 % ) Sampling Time: 00:56:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22838661 Comparison Time: 24:16:39 (hh:mm:ss) Elapsed Time, 334642 HSPs Collected Number of families returned by RECON: 34690 Round Time: 25:45:36 (hh:mm:ss) Elapsed Time : 417 families discovered. RepeatScout/RECON discovery complete: 987 families found Classification Time: 00:54:01 (hh:mm:ss) Elapsed Time Program Time: 31:33:46 (hh:mm:ss) Elapsed Time