RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.rc8y55/RM_21390.SatNov252137422023 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: 1700977059 Database = /dev/shm/rModeler.rc8y55/GCA_004011185.1_bStrHab1_v1.h - Sequences = 3728 - Bases = 285706558 - N50 = 154306 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 1413820-1514727 | [ 1 ] 1312914-1413820 | [ ] 1212007-1312913 | [ 1 ] 1111101-1212007 | [ 3 ] 1010195-1111101 | [ 3 ] 909288-1010194 | [ 6 ] 808382-909288 | [ 4 ] 707475-808381 | [ 8 ] 606569-707475 | [ 8 ] 505663-606569 | [ 17 ] 404756-505662 | [ 30 ] 303850-404756 |* [ 82 ] 202943-303849 |** [ 137 ] 102037-202943 |******* [ 421 ] 1131-102037 |************************************************** [ 3007 ] Storage Throughput = excellent ( 1177.41 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40010026 bp ( 40009528 non ambiguous ) - Num Contigs Represented = 987 - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:35 (hh:mm:ss) Elapsed Time Round Time: 00:27:34 (hh:mm:ss) Elapsed Time : 42 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2243 repeats masked totaling 687426 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10026371 bp Num Contigs Represented = 287 Non ambiguous bp: Initial: 10026371 bp After Masking: 9280884 bp Masked: 7.44 % -- Input Database Coverage: 10026371 bp out of 285706558 bp ( 3.51 % ) Sampling Time: 00:00:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 48828 Comparison Time: 00:07:22 (hh:mm:ss) Elapsed Time, 421 HSPs Collected Number of families returned by RECON: 216 Round Time: 00:07:57 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6602 repeats masked totaling 2124992 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30023920 bp Num Contigs Represented = 774 Non ambiguous bp: Initial: 30023422 bp After Masking: 27650380 bp Masked: 7.90 % -- Input Database Coverage: 40050291 bp out of 285706558 bp ( 14.02 % ) Sampling Time: 00:01:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 446040 Comparison Time: 00:39:26 (hh:mm:ss) Elapsed Time, 4346 HSPs Collected Number of families returned by RECON: 1419 Round Time: 00:41:06 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20899 repeats masked totaling 6337239 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90022000 bp Num Contigs Represented = 1825 Non ambiguous bp: Initial: 90019018 bp After Masking: 83040215 bp Masked: 7.75 % -- Input Database Coverage: 130072291 bp out of 285706558 bp ( 45.53 % ) Sampling Time: 00:03:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3927003 Comparison Time: 04:43:51 (hh:mm:ss) Elapsed Time, 99303 HSPs Collected Number of families returned by RECON: 9072 Round Time: 04:53:02 (hh:mm:ss) Elapsed Time : 52 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:16 (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... 44892 repeats masked totaling 13276758 bp(s). - TE Masking time 00:01:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 155634007 bp Num Contigs Represented = 2568 Non ambiguous bp: Initial: 155632022 bp After Masking: 141429810 bp Masked: 9.13 % -- Input Database Coverage: 285706298 bp out of 285706558 bp ( 100.00 % ) Sampling Time: 00:06:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 11618610 Comparison Time: 13:22:27 (hh:mm:ss) Elapsed Time, 156345 HSPs Collected Number of families returned by RECON: 21633 Round Time: 13:39:50 (hh:mm:ss) Elapsed Time : 89 families discovered. RepeatScout/RECON discovery complete: 190 families found Classification Time: 00:18:40 (hh:mm:ss) Elapsed Time Program Time: 20:08:09 (hh:mm:ss) Elapsed Time