RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Hmm9AF/RM_3300872.MonDec41505052023 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: 1701731105 Database = /dev/shm/rModeler.Hmm9AF/GCF_015227805.2_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 ( 1378.34 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 41021281 bp ( 40013076 non ambiguous ) - Num Contigs Represented = 63 - Sequence extraction : 00:02:05 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:34 (hh:mm:ss) Elapsed Time Round Time: 00:20:38 (hh:mm:ss) Elapsed Time : 140 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 00:00:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2553 repeats masked totaling 942346 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10227277 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10003961 bp After Masking: 8928548 bp Masked: 10.75 % -- Input Database Coverage: 10227277 bp out of 1105955550 bp ( 0.92 % ) Sampling Time: 00:00:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:07:32 (hh:mm:ss) Elapsed Time, 858 HSPs Collected Number of families returned by RECON: 340 Round Time: 00:08:36 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8146 repeats masked totaling 2743776 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30793924 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 30009035 bp After Masking: 26751956 bp Masked: 10.85 % -- Input Database Coverage: 41021201 bp out of 1105955550 bp ( 3.71 % ) Sampling Time: 00:03:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 301476 Comparison Time: 00:39:02 (hh:mm:ss) Elapsed Time, 6683 HSPs Collected Number of families returned by RECON: 1924 Round Time: 00:42:40 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 24787 repeats masked totaling 8275465 bp(s). - TE Masking time 00:00:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 92149621 bp Num Contigs Represented = 115 Non ambiguous bp: Initial: 90013013 bp After Masking: 80328391 bp Masked: 10.76 % -- Input Database Coverage: 133170822 bp out of 1105955550 bp ( 12.04 % ) Sampling Time: 00:09:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2706301 Comparison Time: 04:43:33 (hh:mm:ss) Elapsed Time, 83539 HSPs Collected Number of families returned by RECON: 10990 Round Time: 04:56:00 (hh:mm:ss) Elapsed Time : 85 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 84423 repeats masked totaling 29067267 bp(s). - TE Masking time 00:03:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 276981011 bp Num Contigs Represented = 242 Non ambiguous bp: Initial: 270033336 bp After Masking: 236728236 bp Masked: 12.33 % -- Input Database Coverage: 410151833 bp out of 1105955550 bp ( 37.09 % ) Sampling Time: 00:26:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24545521 Comparison Time: 37:04:48 (hh:mm:ss) Elapsed Time, 298722 HSPs Collected Number of families returned by RECON: 69662 Round Time: 38:29:19 (hh:mm:ss) Elapsed Time : 246 families discovered. RepeatScout/RECON discovery complete: 476 families found Classification Time: 00:34:56 (hh:mm:ss) Elapsed Time Program Time: 45:12:09 (hh:mm:ss) Elapsed Time