RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.vV19mV/RM_1615064.MonJan150842242024 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: 1705336941 Database = /dev/shm/rModeler.vV19mV/GCF_029281585.1_NHGRI_mGorGor1-v1.1-0.2.freeze_pri - Sequences = 637 - Bases = 3600562452 - N50 = 153954438 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 232926936-249563974 | [ 1 ] 216289898-232926935 | [ ] 199652860-216289897 | [ 2 ] 183015822-199652859 | [ 2 ] 166378784-183015821 | [ 2 ] 149741746-166378783 | [ 3 ] 133104708-149741745 | [ 4 ] 116467671-133104708 | [ 3 ] 99830633-116467670 | [ 2 ] 83193595-99830632 | [ 2 ] 66556557-83193594 | [ 1 ] 49919519-66556556 | [ 3 ] 33282481-49919518 | [ ] 16645443-33282480 | [ 1 ] 8406-16645443 |************************************************** [ 611 ] Storage Throughput = excellent ( 1004.97 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40099055 bp ( 40018955 non ambiguous ) - Num Contigs Represented = 58 - Sequence extraction : 00:02:12 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:10 (hh:mm:ss) Elapsed Time Round Time: 00:30:41 (hh:mm:ss) Elapsed Time : 218 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11215 repeats masked totaling 2667392 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001106 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10001106 bp After Masking: 5573983 bp Masked: 44.27 % -- Input Database Coverage: 10001106 bp out of 3600562452 bp ( 0.28 % ) Sampling Time: 00:07:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:09:45 (hh:mm:ss) Elapsed Time, 6785 HSPs Collected Number of families returned by RECON: 854 Round Time: 00:18:00 (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 : 00:01:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:24:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 35641 repeats masked totaling 8627515 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30097869 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 30017769 bp After Masking: 15536951 bp Masked: 48.24 % -- Input Database Coverage: 40098975 bp out of 3600562452 bp ( 1.11 % ) Sampling Time: 00:26:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:27:41 (hh:mm:ss) Elapsed Time, 20392 HSPs Collected Number of families returned by RECON: 1889 Round Time: 00:55:23 (hh:mm:ss) Elapsed Time : 62 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:55:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 120431 repeats masked totaling 27965425 bp(s). - TE Masking time 00:01:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90210834 bp Num Contigs Represented = 84 Non ambiguous bp: Initial: 90036578 bp After Masking: 45850376 bp Masked: 49.08 % -- Input Database Coverage: 130309809 bp out of 3600562452 bp ( 3.62 % ) Sampling Time: 01:02:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 02:19:13 (hh:mm:ss) Elapsed Time, 84092 HSPs Collected Number of families returned by RECON: 6247 Round Time: 03:24:21 (hh:mm:ss) Elapsed Time : 178 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 02:48:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 383734 repeats masked totaling 90438148 bp(s). - TE Masking time 00:05:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270256121 bp Num Contigs Represented = 158 Non ambiguous bp: Initial: 270031191 bp After Masking: 130192498 bp Masked: 51.79 % -- Input Database Coverage: 400565930 bp out of 3600562452 bp ( 11.13 % ) Sampling Time: 03:08:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22953700 Comparison Time: 16:22:26 (hh:mm:ss) Elapsed Time, 294901 HSPs Collected Number of families returned by RECON: 24649 Round Time: 19:46:21 (hh:mm:ss) Elapsed Time : 410 families discovered. RepeatScout/RECON discovery complete: 886 families found Classification Time: 00:36:30 (hh:mm:ss) Elapsed Time Program Time: 25:31:16 (hh:mm:ss) Elapsed Time