RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.Z5mMun/RM_22786.WedDec40621552024 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: 1733322114 Database = /scratch/tmp/rModeler.Z5mMun/GCA_030445055.2_mDasNov1.1.hap1 - Sequences = 588 - Bases = 3296222425 - N50 = 127761625 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 196419940-210449487 | [ 2 ] 182390393-196419939 | [ 1 ] 168360846-182390392 | [ 1 ] 154331299-168360845 | [ 1 ] 140301753-154331299 | [ ] 126272206-140301752 | [ 5 ] 112242659-126272205 | [ 3 ] 98213112-112242658 | [ 3 ] 84183565-98213111 | [ 1 ] 70154019-84183565 | [ 5 ] 56124472-70154018 | [ 4 ] 42094925-56124471 | [ 1 ] 28065378-42094924 | [ 4 ] 14035831-28065377 | [ ] 6285-14035831 |************************************************** [ 557 ] Storage Throughput = fair ( 596.95 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40495220 bp ( 40000999 non ambiguous ) - Num Contigs Represented = 59 - Sequence extraction : 00:02:36 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:12 (hh:mm:ss) Elapsed Time Round Time: 00:36:15 (hh:mm:ss) Elapsed Time : 348 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13489 repeats masked totaling 4098649 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10126599 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 10012731 bp After Masking: 5807569 bp Masked: 42.00 % -- Input Database Coverage: 10126599 bp out of 3296222425 bp ( 0.31 % ) Sampling Time: 00:01:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:04:47 (hh:mm:ss) Elapsed Time, 7784 HSPs Collected Number of families returned by RECON: 801 Round Time: 00:06:49 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44399 repeats masked totaling 12791643 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30408534 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 30028181 bp After Masking: 16958866 bp Masked: 43.52 % -- Input Database Coverage: 40535133 bp out of 3296222425 bp ( 1.23 % ) Sampling Time: 00:03:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:24:32 (hh:mm:ss) Elapsed Time, 21642 HSPs Collected Number of families returned by RECON: 2222 Round Time: 00:30:03 (hh:mm:ss) Elapsed Time : 57 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 143622 repeats masked totaling 41109805 bp(s). - TE Masking time 00:02:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90815475 bp Num Contigs Represented = 73 Non ambiguous bp: Initial: 90020908 bp After Masking: 48263162 bp Masked: 46.39 % -- Input Database Coverage: 131350608 bp out of 3296222425 bp ( 3.98 % ) Sampling Time: 00:11:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2591226 Comparison Time: 02:39:23 (hh:mm:ss) Elapsed Time, 88318 HSPs Collected Number of families returned by RECON: 7098 Round Time: 02:58:48 (hh:mm:ss) Elapsed Time : 183 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:17:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 458725 repeats masked totaling 130154597 bp(s). - TE Masking time 00:08:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272172820 bp Num Contigs Represented = 144 Non ambiguous bp: Initial: 270008168 bp After Masking: 137699705 bp Masked: 49.00 % -- Input Database Coverage: 403523428 bp out of 3296222425 bp ( 12.24 % ) Sampling Time: 00:35:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23348361 Comparison Time: 20:06:23 (hh:mm:ss) Elapsed Time, 243407 HSPs Collected Number of families returned by RECON: 25258 Round Time: 21:29:23 (hh:mm:ss) Elapsed Time : 451 families discovered. RepeatScout/RECON discovery complete: 1048 families found Classification Time: 00:59:40 (hh:mm:ss) Elapsed Time Program Time: 26:40:58 (hh:mm:ss) Elapsed Time