RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Foljwd/RM_810.TueNov280318542023 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: 1701170334 Database = /dev/shm/rModeler.Foljwd/GCA_028017835.1_rEmyOrb1.hap1 - Sequences = 106 - Bases = 2309740635 - N50 = 158421364 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 348960482-373885020 | [ 1 ] 324035945-348960482 | [ ] 299111408-324035945 | [ 1 ] 274186871-299111408 | [ ] 249262334-274186871 | [ ] 224337796-249262333 | [ ] 199413259-224337796 | [ 1 ] 174488722-199413259 | [ ] 149564185-174488722 | [ 1 ] 124639648-149564185 |* [ 3 ] 99715110-124639647 |* [ 2 ] 74790573-99715110 |* [ 2 ] 49866036-74790573 |* [ 2 ] 24941499-49866036 |*** [ 6 ] 16962-24941499 |************************************************** [ 87 ] Storage Throughput = excellent ( 1174.56 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40035583 bp ( 40028498 non ambiguous ) - Num Contigs Represented = 33 - Sequence extraction : 00:03:33 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:18 (hh:mm:ss) Elapsed Time Round Time: 00:32:18 (hh:mm:ss) Elapsed Time : 626 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14413 repeats masked totaling 3263632 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001246 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10001246 bp After Masking: 6605207 bp Masked: 33.96 % -- Input Database Coverage: 10001246 bp out of 2309740635 bp ( 0.43 % ) Sampling Time: 00:01:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:06:03 (hh:mm:ss) Elapsed Time, 11975 HSPs Collected Number of families returned by RECON: 1584 Round Time: 00:08:18 (hh:mm:ss) Elapsed Time : 35 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46591 repeats masked totaling 10197880 bp(s). - TE Masking time 00:00:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30034257 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 30027172 bp After Masking: 19538394 bp Masked: 34.93 % -- Input Database Coverage: 40035503 bp out of 2309740635 bp ( 1.73 % ) Sampling Time: 00:04:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:31:23 (hh:mm:ss) Elapsed Time, 63022 HSPs Collected Number of families returned by RECON: 4855 Round Time: 00:39:11 (hh:mm:ss) Elapsed Time : 141 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:08:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 153013 repeats masked totaling 34012188 bp(s). - TE Masking time 00:02:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90147622 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 90017523 bp After Masking: 55096027 bp Masked: 38.79 % -- Input Database Coverage: 130183125 bp out of 2309740635 bp ( 5.64 % ) Sampling Time: 00:15:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 02:58:15 (hh:mm:ss) Elapsed Time, 287040 HSPs Collected Number of families returned by RECON: 14024 Round Time: 03:26:53 (hh:mm:ss) Elapsed Time : 451 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:23:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 532450 repeats masked totaling 115670891 bp(s). - TE Masking time 00:13:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270630570 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 270006279 bp After Masking: 151223674 bp Masked: 43.99 % -- Input Database Coverage: 400813695 bp out of 2309740635 bp ( 17.35 % ) Sampling Time: 00:48:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22933378 Comparison Time: 21:53:29 (hh:mm:ss) Elapsed Time, 1228363 HSPs Collected Number of families returned by RECON: 44678 Round Time: 24:04:00 (hh:mm:ss) Elapsed Time : 1134 families discovered. RepeatScout/RECON discovery complete: 2387 families found Classification Time: 01:43:34 (hh:mm:ss) Elapsed Time Program Time: 30:34:14 (hh:mm:ss) Elapsed Time