RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.dVj5eq/RM_1518419.SatDec21233162023 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: 1701549196 Database = /dev/shm/rModeler.dVj5eq/GCF_023638135.1_bFalBia1.pri - Sequences = 397 - Bases = 1285492283 - N50 = 92830268 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 118873965-127364718 | [ 3 ] 110383213-118873965 | [ 1 ] 101892461-110383213 | [ ] 93401708-101892460 | [ ] 84910956-93401708 | [ 2 ] 76420204-84910956 | [ 1 ] 67929452-76420204 | [ 1 ] 59438699-67929451 | [ 1 ] 50947947-59438699 | [ 1 ] 42457195-50947947 | [ ] 33966443-42457195 | [ 3 ] 25475690-33966442 | [ 1 ] 16984938-25475690 | [ 3 ] 8494186-16984938 | [ 1 ] 3434-8494186 |************************************************** [ 379 ] Storage Throughput = good ( 739.55 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40073328 bp ( 40004942 non ambiguous ) - Num Contigs Represented = 85 - Sequence extraction : 00:01:38 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:25 (hh:mm:ss) Elapsed Time Round Time: 00:22:59 (hh:mm:ss) Elapsed Time : 62 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1274 repeats masked totaling 449894 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10025288 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 10025288 bp After Masking: 8915812 bp Masked: 11.07 % -- Input Database Coverage: 10025288 bp out of 1285492283 bp ( 0.78 % ) Sampling Time: 00:01:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:33 (hh:mm:ss) Elapsed Time, 428 HSPs Collected Number of families returned by RECON: 214 Round Time: 00:08:08 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4120 repeats masked totaling 1311244 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30087960 bp Num Contigs Represented = 71 Non ambiguous bp: Initial: 30019574 bp After Masking: 26731447 bp Masked: 10.95 % -- Input Database Coverage: 40113248 bp out of 1285492283 bp ( 3.12 % ) Sampling Time: 00:04:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:41:21 (hh:mm:ss) Elapsed Time, 5177 HSPs Collected Number of families returned by RECON: 1434 Round Time: 00:45:52 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13257 repeats masked totaling 4311486 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90368452 bp Num Contigs Represented = 135 Non ambiguous bp: Initial: 90028687 bp After Masking: 80062784 bp Masked: 11.07 % -- Input Database Coverage: 130481700 bp out of 1285492283 bp ( 10.15 % ) Sampling Time: 00:16:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2609470 Comparison Time: 03:56:52 (hh:mm:ss) Elapsed Time, 42329 HSPs Collected Number of families returned by RECON: 8830 Round Time: 04:16:12 (hh:mm:ss) Elapsed Time : 71 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:28:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 48937 repeats masked totaling 16324676 bp(s). - TE Masking time 00:02:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270529687 bp Num Contigs Represented = 253 Non ambiguous bp: Initial: 270020809 bp After Masking: 235297934 bp Masked: 12.86 % -- Input Database Coverage: 401011387 bp out of 1285492283 bp ( 31.20 % ) Sampling Time: 00:42:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23096206 Comparison Time: 30:12:38 (hh:mm:ss) Elapsed Time, 176346 HSPs Collected Number of families returned by RECON: 57475 Round Time: 31:43:33 (hh:mm:ss) Elapsed Time : 193 families discovered. RepeatScout/RECON discovery complete: 341 families found Classification Time: 00:34:59 (hh:mm:ss) Elapsed Time Program Time: 37:51:43 (hh:mm:ss) Elapsed Time