RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.AVLWZc/RM_3122.ThuNov301105142023 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: 1701371112 Database = /dev/shm/rModeler.AVLWZc/GCA_029931755.1_rEulEur1.hap2 - Sequences = 381 - Bases = 1775520415 - N50 = 109232959 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 170094742-182244296 | [ 1 ] 157945189-170094742 | [ ] 145795636-157945189 | [ ] 133646083-145795636 | [ 1 ] 121496530-133646083 | [ 2 ] 109346977-121496530 | [ 1 ] 97197424-109346977 | [ 3 ] 85047871-97197424 | [ 1 ] 72898318-85047871 | [ 2 ] 60748765-72898318 | [ 3 ] 48599212-60748765 | [ 3 ] 36449659-48599212 | [ 2 ] 24300106-36449659 | [ 1 ] 12150553-24300106 | [ 1 ] 1000-12150553 |************************************************** [ 360 ] Storage Throughput = excellent ( 1147.98 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40150276 bp ( 40036851 non ambiguous ) - Num Contigs Represented = 35 - Sequence extraction : 00:02:07 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:05 (hh:mm:ss) Elapsed Time Round Time: 00:26:25 (hh:mm:ss) Elapsed Time : 633 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21073 repeats masked totaling 3801265 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000336 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 10000336 bp After Masking: 6111528 bp Masked: 38.89 % -- Input Database Coverage: 10000336 bp out of 1775520415 bp ( 0.56 % ) Sampling Time: 00:01:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:55 (hh:mm:ss) Elapsed Time, 7564 HSPs Collected Number of families returned by RECON: 1328 Round Time: 00:07:23 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 65652 repeats masked totaling 11484796 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30149860 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 30036435 bp After Masking: 18260604 bp Masked: 39.21 % -- Input Database Coverage: 40150196 bp out of 1775520415 bp ( 2.26 % ) Sampling Time: 00:03:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:28:55 (hh:mm:ss) Elapsed Time, 46189 HSPs Collected Number of families returned by RECON: 4573 Round Time: 00:36:42 (hh:mm:ss) Elapsed Time : 129 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 211489 repeats masked totaling 37414952 bp(s). - TE Masking time 00:02:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90325691 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 90027144 bp After Masking: 51637617 bp Masked: 42.64 % -- Input Database Coverage: 130475887 bp out of 1775520415 bp ( 7.35 % ) Sampling Time: 00:12:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2568511 Comparison Time: 02:57:07 (hh:mm:ss) Elapsed Time, 237770 HSPs Collected Number of families returned by RECON: 13488 Round Time: 03:23:02 (hh:mm:ss) Elapsed Time : 484 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 698141 repeats masked totaling 124505386 bp(s). - TE Masking time 00:11:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270790986 bp Num Contigs Represented = 104 Non ambiguous bp: Initial: 270016561 bp After Masking: 142446560 bp Masked: 47.25 % -- Input Database Coverage: 401266873 bp out of 1775520415 bp ( 22.60 % ) Sampling Time: 00:40:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23130201 Comparison Time: 22:22:14 (hh:mm:ss) Elapsed Time, 604126 HSPs Collected Number of families returned by RECON: 40816 Round Time: 24:20:19 (hh:mm:ss) Elapsed Time : 1228 families discovered. RepeatScout/RECON discovery complete: 2492 families found Classification Time: 01:26:08 (hh:mm:ss) Elapsed Time Program Time: 30:19:59 (hh:mm:ss) Elapsed Time