RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.L3fp9e/RM_20123.FriFeb71220112025 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: 1738959584 Database = /dev/shm/rModeler.L3fp9e/GCA_045345515.1_bMorGui1_haplotype_2 - Sequences = 544 - Bases = 1576624229 - N50 = 61502442 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 95889121-102737265 | [ 1 ] 89040978-95889121 | [ 1 ] 82192835-89040978 | [ 2 ] 75344691-82192834 | [ 2 ] 68496548-75344691 | [ 1 ] 61648405-68496548 | [ 1 ] 54800261-61648404 | [ 3 ] 47952118-54800261 | [ 5 ] 41103975-47952118 | [ 3 ] 34255831-41103974 | [ 1 ] 27407688-34255831 | [ 3 ] 20559545-27407688 | [ 2 ] 13711401-20559544 | [ ] 6863258-13711401 | [ 3 ] 15115-6863258 |************************************************** [ 516 ] Storage Throughput = excellent ( 1891.15 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40032282 bp ( 40031682 non ambiguous ) - Num Contigs Represented = 99 - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:03 (hh:mm:ss) Elapsed Time Round Time: 00:24:05 (hh:mm:ss) Elapsed Time : 98 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1787 repeats masked totaling 820383 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10018371 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 10018371 bp After Masking: 8094979 bp Masked: 19.20 % -- Input Database Coverage: 10018371 bp out of 1576624229 bp ( 0.64 % ) Sampling Time: 00:02:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 01:56:10 (hh:mm:ss) Elapsed Time, 1256 HSPs Collected Number of families returned by RECON: 289 Round Time: 02:02:31 (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 : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6000 repeats masked totaling 3177510 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30013903 bp Num Contigs Represented = 90 Non ambiguous bp: Initial: 30013303 bp After Masking: 22351933 bp Masked: 25.53 % -- Input Database Coverage: 40032274 bp out of 1576624229 bp ( 2.54 % ) Sampling Time: 00:14:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 06:49:59 (hh:mm:ss) Elapsed Time, 12253 HSPs Collected Number of families returned by RECON: 1135 Round Time: 07:08:19 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:32:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20935 repeats masked totaling 10251787 bp(s). - TE Masking time 00:01:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90028595 bp Num Contigs Represented = 163 Non ambiguous bp: Initial: 90026995 bp After Masking: 67583887 bp Masked: 24.93 % -- Input Database Coverage: 130060869 bp out of 1576624229 bp ( 8.25 % ) Sampling Time: 00:35:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2568511 Comparison Time: 17:46:45 (hh:mm:ss) Elapsed Time, 62382 HSPs Collected Number of families returned by RECON: 6668 Round Time: 18:34:50 (hh:mm:ss) Elapsed Time : 78 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:38:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 74348 repeats masked totaling 35457373 bp(s). - TE Masking time 00:02:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270036274 bp Num Contigs Represented = 258 Non ambiguous bp: Initial: 270030474 bp After Masking: 200192521 bp Masked: 25.86 % -- Input Database Coverage: 400097143 bp out of 1576624229 bp ( 25.38 % ) Sampling Time: 01:44:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23069028 Comparison Time: 39:06:43 (hh:mm:ss) Elapsed Time, 261099 HSPs Collected Number of families returned by RECON: 41040 Round Time: 41:05:19 (hh:mm:ss) Elapsed Time : 261 families discovered. RepeatScout/RECON discovery complete: 451 families found Classification Time: 00:24:40 (hh:mm:ss) Elapsed Time Program Time: 69:39:44 (hh:mm:ss) Elapsed Time