RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.S1ybV3/RM_19854.WedJun260158122024 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: 1719392291 Database = /dev/shm/rModeler.S1ybV3/GCF_029281585.2_NHGRI_mGorGor1-v2.0_pri - Sequences = 26 - Bases = 3545850636 Storage Throughput = excellent ( 1043.10 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001650 bp ( 40001650 non ambiguous ) - Num Contigs Represented = 25 - Sequence extraction : 00:01:41 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:26:29 (hh:mm:ss) Elapsed Time Round Time: 00:47:51 (hh:mm:ss) Elapsed Time : 228 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10785 repeats masked totaling 2631154 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000432 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10000432 bp After Masking: 5371391 bp Masked: 46.29 % -- Input Database Coverage: 10000432 bp out of 3545850636 bp ( 0.28 % ) Sampling Time: 00:10:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:04:40 (hh:mm:ss) Elapsed Time, 5123 HSPs Collected Number of families returned by RECON: 742 Round Time: 00:15:13 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:23:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36229 repeats masked totaling 8775215 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001213 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30001213 bp After Masking: 15742160 bp Masked: 47.53 % -- Input Database Coverage: 40001645 bp out of 3545850636 bp ( 1.13 % ) Sampling Time: 00:25:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:23:09 (hh:mm:ss) Elapsed Time, 21146 HSPs Collected Number of families returned by RECON: 1932 Round Time: 00:49:05 (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 : 00:03:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:05:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 116203 repeats masked totaling 27876006 bp(s). - TE Masking time 00:01:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90043787 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 90003780 bp After Masking: 45895106 bp Masked: 49.01 % -- Input Database Coverage: 130045432 bp out of 3545850636 bp ( 3.67 % ) Sampling Time: 01:11:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 02:31:15 (hh:mm:ss) Elapsed Time, 85522 HSPs Collected Number of families returned by RECON: 6332 Round Time: 03:45:48 (hh:mm:ss) Elapsed Time : 188 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 02:56:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 382841 repeats masked totaling 92291016 bp(s). - TE Masking time 00:07:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270137331 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 270017310 bp After Masking: 132749249 bp Masked: 50.84 % -- Input Database Coverage: 400182763 bp out of 3545850636 bp ( 11.29 % ) Sampling Time: 03:15:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22818390 Comparison Time: 19:19:18 (hh:mm:ss) Elapsed Time, 218456 HSPs Collected Number of families returned by RECON: 26246 Round Time: 22:55:10 (hh:mm:ss) Elapsed Time : 372 families discovered. RepeatScout/RECON discovery complete: 866 families found Classification Time: 00:39:44 (hh:mm:ss) Elapsed Time Program Time: 29:12:51 (hh:mm:ss) Elapsed Time