RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.at55ey/RM_3260166.SunJan140356282024 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: 1705233388 Database = /dev/shm/rModeler.at55ey/GCF_028885625.1_NHGRI_mPonPyg2-v1.1-hic.freeze_pri - Sequences = 1554 - Bases = 3249335160 - N50 = 140978198 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 214439072-229755851 | [ 1 ] 199122293-214439071 | [ 1 ] 183805515-199122293 | [ 2 ] 168488736-183805514 | [ 1 ] 153171958-168488736 | [ 3 ] 137855179-153171957 | [ 3 ] 122538401-137855179 | [ 2 ] 107221622-122538400 | [ 2 ] 91904844-107221622 | [ 2 ] 76588065-91904843 | [ 3 ] 61271287-76588065 | [ 2 ] 45954508-61271286 | [ 1 ] 30637730-45954508 | [ 2 ] 15320951-30637729 | [ ] 4173-15320951 |************************************************** [ 1529 ] Storage Throughput = excellent ( 1140.49 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40055267 bp ( 40013266 non ambiguous ) - Num Contigs Represented = 81 - Sequence extraction : 00:02:19 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:13 (hh:mm:ss) Elapsed Time Round Time: 00:47:43 (hh:mm:ss) Elapsed Time : 274 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12591 repeats masked totaling 3037931 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10070363 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 10029362 bp After Masking: 6276033 bp Masked: 37.42 % -- Input Database Coverage: 10070363 bp out of 3249335160 bp ( 0.31 % ) Sampling Time: 00:04:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:07:15 (hh:mm:ss) Elapsed Time, 6893 HSPs Collected Number of families returned by RECON: 951 Round Time: 00:12:11 (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 : 00:01:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 38820 repeats masked totaling 9739074 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30024824 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 30023824 bp After Masking: 17691486 bp Masked: 41.08 % -- Input Database Coverage: 40095187 bp out of 3249335160 bp ( 1.23 % ) Sampling Time: 00:11:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:42:24 (hh:mm:ss) Elapsed Time, 26615 HSPs Collected Number of families returned by RECON: 2459 Round Time: 00:55:23 (hh:mm:ss) Elapsed Time : 78 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 133146 repeats masked totaling 31995731 bp(s). - TE Masking time 00:01:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90137245 bp Num Contigs Represented = 132 Non ambiguous bp: Initial: 90025304 bp After Masking: 50878629 bp Masked: 43.48 % -- Input Database Coverage: 130232432 bp out of 3249335160 bp ( 4.01 % ) Sampling Time: 00:32:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2575315 Comparison Time: 02:57:23 (hh:mm:ss) Elapsed Time, 95427 HSPs Collected Number of families returned by RECON: 7366 Round Time: 03:33:28 (hh:mm:ss) Elapsed Time : 175 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:15:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 438943 repeats masked totaling 103847253 bp(s). - TE Masking time 00:06:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270359744 bp Num Contigs Represented = 285 Non ambiguous bp: Initial: 270005460 bp After Masking: 143679075 bp Masked: 46.79 % -- Input Database Coverage: 400592176 bp out of 3249335160 bp ( 12.33 % ) Sampling Time: 01:37:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23259610 Comparison Time: 21:05:12 (hh:mm:ss) Elapsed Time, 402179 HSPs Collected Number of families returned by RECON: 29630 Round Time: 23:01:23 (hh:mm:ss) Elapsed Time : 399 families discovered. RepeatScout/RECON discovery complete: 944 families found Classification Time: 00:38:46 (hh:mm:ss) Elapsed Time Program Time: 29:08:54 (hh:mm:ss) Elapsed Time