RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.P2gWcU/RM_6224.SunJan150825252023 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: 1673799924 Database = /dev/shm/rModeler.P2gWcU/GCF_015852505.1_mTacAcu1.pri - Sequences = 310 - Bases = 2213004214 - N50 = 66300460 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 164662256-176423766 | [ 2 ] 152900746-164662255 | [ ] 141139237-152900746 | [ ] 129377727-141139236 | [ 2 ] 117616217-129377726 | [ ] 105854708-117616217 | [ 2 ] 94093198-105854707 | [ ] 82331688-94093197 | [ 1 ] 70570179-82331688 | [ 1 ] 58808669-70570178 |* [ 8 ] 47047159-58808668 | [ 1 ] 35285650-47047159 | [ 5 ] 23524140-35285649 |* [ 7 ] 11762630-23524139 | [ 5 ] 1121-11762630 |************************************************** [ 276 ] Storage Throughput = excellent ( 1049.05 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40518730 bp ( 40020037 non ambiguous ) - Num Contigs Represented = 78 - Sequence extraction : 00:01:50 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:18 (hh:mm:ss) Elapsed Time Round Time: 00:36:55 (hh:mm:ss) Elapsed Time : 306 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:30 (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... 39603 repeats masked totaling 5607434 bp(s). - TE Masking time 00:00:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10301279 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 10019627 bp After Masking: 4062337 bp Masked: 59.46 % -- Input Database Coverage: 10301279 bp out of 2213004214 bp ( 0.47 % ) Sampling Time: 00:02:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33670 Comparison Time: 00:06:51 (hh:mm:ss) Elapsed Time, 2149 HSPs Collected Number of families returned by RECON: 272 Round Time: 00:09:07 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 120792 repeats masked totaling 17086380 bp(s). - TE Masking time 00:02:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30217371 bp Num Contigs Represented = 69 Non ambiguous bp: Initial: 30000330 bp After Masking: 11940654 bp Masked: 60.20 % -- Input Database Coverage: 40518650 bp out of 2213004214 bp ( 1.83 % ) Sampling Time: 00:05:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:27:51 (hh:mm:ss) Elapsed Time, 28994 HSPs Collected Number of families returned by RECON: 1349 Round Time: 00:36:33 (hh:mm:ss) Elapsed Time : 35 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 367174 repeats masked totaling 52761026 bp(s). - TE Masking time 00:08:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91458386 bp Num Contigs Represented = 105 Non ambiguous bp: Initial: 90013374 bp After Masking: 34337467 bp Masked: 61.85 % -- Input Database Coverage: 131977036 bp out of 2213004214 bp ( 5.96 % ) Sampling Time: 00:16:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2623195 Comparison Time: 02:25:47 (hh:mm:ss) Elapsed Time, 75416 HSPs Collected Number of families returned by RECON: 4604 Round Time: 02:44:44 (hh:mm:ss) Elapsed Time : 90 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1136059 repeats masked totaling 161471442 bp(s). - TE Masking time 00:25:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 273714675 bp Num Contigs Represented = 161 Non ambiguous bp: Initial: 270004714 bp After Masking: 100072808 bp Masked: 62.94 % -- Input Database Coverage: 405691711 bp out of 2213004214 bp ( 18.33 % ) Sampling Time: 00:53:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23574411 Comparison Time: 16:39:06 (hh:mm:ss) Elapsed Time, 628779 HSPs Collected Number of families returned by RECON: 17412 Round Time: 17:47:02 (hh:mm:ss) Elapsed Time : 336 families discovered. RepeatScout/RECON discovery complete: 773 families found Classification Time: 00:25:00 (hh:mm:ss) Elapsed Time Program Time: 22:19:21 (hh:mm:ss) Elapsed Time