RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.e08MsV/RM_883394.FriFeb142046172025 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: 1739594776 Database = /dev/shm/rModeler.e08MsV/GCA_905221625.1_Smic_CassKB8 - Sequences = 67937 - Bases = 813744491 - N50 = 42997 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 353458-378634 | [ 3 ] 328282-353457 | [ 1 ] 303107-328282 | [ 1 ] 277931-303106 | [ 8 ] 252756-277931 | [ 15 ] 227580-252755 | [ 24 ] 202404-227579 | [ 46 ] 177229-202404 | [ 79 ] 152053-177228 | [ 148 ] 126878-152053 | [ 249 ] 101702-126877 | [ 441 ] 76526-101701 | [ 980 ] 51351-76526 |* [ 1976 ] 26175-51350 |*** [ 4574 ] 1000-26175 |************************************************** [ 59392 ] Storage Throughput = excellent ( 1712.96 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40459341 bp ( 40007143 non ambiguous ) - Num Contigs Represented = 3769 - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:23 (hh:mm:ss) Elapsed Time Round Time: 00:07:07 (hh:mm:ss) Elapsed Time : 105 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7649 repeats masked totaling 652148 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10114028 bp Num Contigs Represented = 987 Non ambiguous bp: Initial: 10002084 bp After Masking: 8688005 bp Masked: 13.14 % -- Input Database Coverage: 10114028 bp out of 813744491 bp ( 1.24 % ) Sampling Time: 00:00:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 487578 Comparison Time: 00:05:25 (hh:mm:ss) Elapsed Time, 37503 HSPs Collected Number of families returned by RECON: 1897 Round Time: 00:06:28 (hh:mm:ss) Elapsed Time : 24 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 29154 repeats masked totaling 3123439 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30345237 bp Num Contigs Represented = 2795 Non ambiguous bp: Initial: 30004983 bp After Masking: 25024225 bp Masked: 16.60 % -- Input Database Coverage: 40459265 bp out of 813744491 bp ( 4.97 % ) Sampling Time: 00:01:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3929806 Comparison Time: 00:20:34 (hh:mm:ss) Elapsed Time, 29596 HSPs Collected Number of families returned by RECON: 5162 Round Time: 00:22:10 (hh:mm:ss) Elapsed Time : 22 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 94586 repeats masked totaling 10095209 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91049730 bp Num Contigs Represented = 8277 Non ambiguous bp: Initial: 90011032 bp After Masking: 74334144 bp Masked: 17.42 % -- Input Database Coverage: 131508995 bp out of 813744491 bp ( 16.16 % ) Sampling Time: 00:03:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 35545096 Comparison Time: 01:52:03 (hh:mm:ss) Elapsed Time, 199429 HSPs Collected Number of families returned by RECON: 22708 Round Time: 02:00:22 (hh:mm:ss) Elapsed Time : 164 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 324769 repeats masked totaling 36717155 bp(s). - TE Masking time 00:02:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 273129352 bp Num Contigs Represented = 24069 Non ambiguous bp: Initial: 270008213 bp After Masking: 216762366 bp Masked: 19.72 % -- Input Database Coverage: 404638347 bp out of 813744491 bp ( 49.73 % ) Sampling Time: 00:10:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 320411955 Comparison Time: 12:15:30 (hh:mm:ss) Elapsed Time, 877375 HSPs Collected Number of families returned by RECON: 89921 Round Time: 13:24:42 (hh:mm:ss) Elapsed Time : 608 families discovered. RepeatScout/RECON discovery complete: 923 families found Classification Time: 00:24:29 (hh:mm:ss) Elapsed Time Program Time: 16:25:18 (hh:mm:ss) Elapsed Time