RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.BO9x1G/RM_2570795.SunApr130256222025 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: 1744538182 Database = /dev/shm/rModeler.BO9x1G/GCA_046129695.1_bLonStr1.mat - Sequences = 161 - Bases = 1207550942 - N50 = 76977286 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 146829409-157315129 | [ 1 ] 136343690-146829409 | [ ] 125857971-136343690 | [ ] 115372252-125857971 | [ 1 ] 104886533-115372252 | [ 1 ] 94400814-104886533 | [ ] 83915095-94400814 | [ 1 ] 73429376-83915095 | [ 1 ] 62943657-73429376 | [ 2 ] 52457938-62943657 | [ ] 41972219-52457938 | [ ] 31486500-41972219 | [ 2 ] 21000781-31486500 |** [ 6 ] 10515062-21000781 |*** [ 9 ] 29343-10515062 |************************************************* [ 137 ] Storage Throughput = excellent ( 1788.74 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001212 bp ( 40000612 non ambiguous ) - Num Contigs Represented = 69 - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:45 (hh:mm:ss) Elapsed Time Round Time: 00:15:11 (hh:mm:ss) Elapsed Time : 145 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3681 repeats masked totaling 1074576 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10032311 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 10032111 bp After Masking: 8310626 bp Masked: 17.16 % -- Input Database Coverage: 10032311 bp out of 1207550942 bp ( 0.83 % ) Sampling Time: 00:00:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:29 (hh:mm:ss) Elapsed Time, 6672 HSPs Collected Number of families returned by RECON: 265 Round Time: 00:04:26 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10280 repeats masked totaling 3479982 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30008794 bp Num Contigs Represented = 64 Non ambiguous bp: Initial: 30008394 bp After Masking: 24728294 bp Masked: 17.60 % -- Input Database Coverage: 40041105 bp out of 1207550942 bp ( 3.32 % ) Sampling Time: 00:02:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:17:13 (hh:mm:ss) Elapsed Time, 49771 HSPs Collected Number of families returned by RECON: 1409 Round Time: 00:19:41 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31783 repeats masked totaling 10378955 bp(s). - TE Masking time 00:00:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90023058 bp Num Contigs Represented = 93 Non ambiguous bp: Initial: 90019558 bp After Masking: 73394999 bp Masked: 18.47 % -- Input Database Coverage: 130064163 bp out of 1207550942 bp ( 10.77 % ) Sampling Time: 00:07:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 01:49:54 (hh:mm:ss) Elapsed Time, 441649 HSPs Collected Number of families returned by RECON: 8623 Round Time: 01:59:09 (hh:mm:ss) Elapsed Time : 107 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 101506 repeats masked totaling 33160983 bp(s). - TE Masking time 00:01:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270027454 bp Num Contigs Represented = 115 Non ambiguous bp: Initial: 270021654 bp After Masking: 219265073 bp Masked: 18.80 % -- Input Database Coverage: 400091617 bp out of 1207550942 bp ( 33.13 % ) Sampling Time: 00:19:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22845420 Comparison Time: 12:36:07 (hh:mm:ss) Elapsed Time, 2294007 HSPs Collected Number of families returned by RECON: 59109 Round Time: 13:25:36 (hh:mm:ss) Elapsed Time : 242 families discovered. RepeatScout/RECON discovery complete: 510 families found Classification Time: 00:22:19 (hh:mm:ss) Elapsed Time Program Time: 16:26:22 (hh:mm:ss) Elapsed Time