RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.VR9ZqM/RM_392922.SunMay71118052023 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: 1683483484 Database = /dev/shm/rModeler.VR9ZqM/GCA_015227805.3_bHirRus1.pri.v3 - Sequences = 617 - Bases = 1105955550 - N50 = 90132487 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 145633387-156035725 | [ 1 ] 135231050-145633387 | [ ] 124828713-135231050 | [ ] 114426376-124828713 | [ 2 ] 104024039-114426376 | [ ] 93621702-104024039 | [ ] 83219365-93621702 | [ 1 ] 72817027-83219364 | [ 2 ] 62414690-72817027 | [ 1 ] 52012353-62414690 | [ ] 41610016-52012353 | [ ] 31207679-41610016 | [ 4 ] 20805342-31207679 | [ 3 ] 10403005-20805342 | [ 8 ] 668-10403005 |************************************************** [ 595 ] Storage Throughput = excellent ( 1477.93 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 41275191 bp ( 40023167 non ambiguous ) - Num Contigs Represented = 77 - Sequence extraction : 00:01:19 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:02 (hh:mm:ss) Elapsed Time Round Time: 00:18:13 (hh:mm:ss) Elapsed Time : 152 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2799 repeats masked totaling 975161 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10388335 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 10023754 bp After Masking: 8872093 bp Masked: 11.49 % -- Input Database Coverage: 10388335 bp out of 1105955550 bp ( 0.94 % ) Sampling Time: 00:00:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 35511 Comparison Time: 00:10:50 (hh:mm:ss) Elapsed Time, 767 HSPs Collected Number of families returned by RECON: 350 Round Time: 00:11:41 (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 : 00:00:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8696 repeats masked totaling 2937133 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30926776 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 30039333 bp After Masking: 26636442 bp Masked: 11.33 % -- Input Database Coverage: 41315111 bp out of 1105955550 bp ( 3.74 % ) Sampling Time: 00:02:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 306936 Comparison Time: 00:41:31 (hh:mm:ss) Elapsed Time, 5982 HSPs Collected Number of families returned by RECON: 1691 Round Time: 00:44:05 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26458 repeats masked totaling 8941829 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 92281265 bp Num Contigs Represented = 101 Non ambiguous bp: Initial: 90008044 bp After Masking: 79643862 bp Masked: 11.51 % -- Input Database Coverage: 133596376 bp out of 1105955550 bp ( 12.08 % ) Sampling Time: 00:06:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2722611 Comparison Time: 03:35:34 (hh:mm:ss) Elapsed Time, 55241 HSPs Collected Number of families returned by RECON: 10980 Round Time: 03:44:07 (hh:mm:ss) Elapsed Time : 77 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 86742 repeats masked totaling 28933030 bp(s). - TE Masking time 00:01:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 276364210 bp Num Contigs Represented = 235 Non ambiguous bp: Initial: 270002248 bp After Masking: 236927108 bp Masked: 12.25 % -- Input Database Coverage: 409960586 bp out of 1105955550 bp ( 37.07 % ) Sampling Time: 00:19:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24405591 Comparison Time: 24:18:26 (hh:mm:ss) Elapsed Time, 273192 HSPs Collected Number of families returned by RECON: 70241 Round Time: 25:16:43 (hh:mm:ss) Elapsed Time : 242 families discovered. RepeatScout/RECON discovery complete: 476 families found Classification Time: 00:23:03 (hh:mm:ss) Elapsed Time Program Time: 30:37:52 (hh:mm:ss) Elapsed Time