RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.RGL4yw/RM_107066.ThuJan121204302023 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: 1673553869 Database = /dev/shm/rModeler.RGL4yw/GCA_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 = excellent ( 1130.81 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40024267 bp ( 40010992 non ambiguous ) - Num Contigs Represented = 84 - Sequence extraction : 00:02:04 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:23:54 (hh:mm:ss) Elapsed Time Round Time: 00:38:40 (hh:mm:ss) Elapsed Time : 53 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1431 repeats masked totaling 565413 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10016387 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 10008779 bp After Masking: 8742790 bp Masked: 12.65 % -- Input Database Coverage: 10016387 bp out of 1285492283 bp ( 0.78 % ) Sampling Time: 00:01:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:44 (hh:mm:ss) Elapsed Time, 629 HSPs Collected Number of families returned by RECON: 266 Round Time: 00:08:12 (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 : 00:01:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3878 repeats masked totaling 1445575 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30007800 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 30002133 bp After Masking: 26491394 bp Masked: 11.70 % -- Input Database Coverage: 40024187 bp out of 1285492283 bp ( 3.11 % ) Sampling Time: 00:04:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:34:32 (hh:mm:ss) Elapsed Time, 4724 HSPs Collected Number of families returned by RECON: 1502 Round Time: 00:39:28 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13317 repeats masked totaling 4414249 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90219862 bp Num Contigs Represented = 138 Non ambiguous bp: Initial: 90029362 bp After Masking: 79723333 bp Masked: 11.45 % -- Input Database Coverage: 130244049 bp out of 1285492283 bp ( 10.13 % ) Sampling Time: 00:15:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2575315 Comparison Time: 04:14:46 (hh:mm:ss) Elapsed Time, 50345 HSPs Collected Number of families returned by RECON: 8727 Round Time: 04:39:08 (hh:mm:ss) Elapsed Time : 72 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:16:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:30:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 48885 repeats masked totaling 16508912 bp(s). - TE Masking time 00:03:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270403344 bp Num Contigs Represented = 245 Non ambiguous bp: Initial: 270029211 bp After Masking: 237246871 bp Masked: 12.14 % -- Input Database Coverage: 400647393 bp out of 1285492283 bp ( 31.17 % ) Sampling Time: 00:51:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23103003 Comparison Time: 31:17:03 (hh:mm:ss) Elapsed Time, 172300 HSPs Collected Number of families returned by RECON: 57705 Round Time: 33:11:46 (hh:mm:ss) Elapsed Time : 216 families discovered. RepeatScout/RECON discovery complete: 351 families found Classification Time: 00:52:50 (hh:mm:ss) Elapsed Time Program Time: 40:10:04 (hh:mm:ss) Elapsed Time