RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.U5L9b4/RM_453567.FriJan191156482024 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: 1705694167 Database = /dev/shm/rModeler.U5L9b4/GCA_029281585.2_NHGRI_mGorGor1-v2.0_pri - Sequences = 25 - Bases = 3545834224 Storage Throughput = good ( 810.44 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40041754 bp ( 40019288 non ambiguous ) - Num Contigs Represented = 25 - Sequence extraction : 00:01:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:08 (hh:mm:ss) Elapsed Time Round Time: 00:41:25 (hh:mm:ss) Elapsed Time : 217 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10119 repeats masked totaling 2584598 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000416 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10000416 bp After Masking: 5600274 bp Masked: 44.00 % -- Input Database Coverage: 10000416 bp out of 3545834224 bp ( 0.28 % ) Sampling Time: 00:07:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:58:46 (hh:mm:ss) Elapsed Time, 4797 HSPs Collected Number of families returned by RECON: 786 Round Time: 01:08:42 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33675 repeats masked totaling 8234153 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30041336 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30018870 bp After Masking: 16036901 bp Masked: 46.58 % -- Input Database Coverage: 40041752 bp out of 3545834224 bp ( 1.13 % ) Sampling Time: 00:13:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 02:09:20 (hh:mm:ss) Elapsed Time, 22877 HSPs Collected Number of families returned by RECON: 2165 Round Time: 02:26:02 (hh:mm:ss) Elapsed Time : 54 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:46:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 115772 repeats masked totaling 27408963 bp(s). - TE Masking time 00:01:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90003962 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 90003962 bp After Masking: 46843372 bp Masked: 47.95 % -- Input Database Coverage: 130045714 bp out of 3545834224 bp ( 3.67 % ) Sampling Time: 00:50:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2530125 Comparison Time: 03:06:52 (hh:mm:ss) Elapsed Time, 109596 HSPs Collected Number of families returned by RECON: 7270 Round Time: 04:02:00 (hh:mm:ss) Elapsed Time : 210 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 02:27:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 387848 repeats masked totaling 92736029 bp(s). - TE Masking time 00:05:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270282538 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 270002503 bp After Masking: 130745873 bp Masked: 51.58 % -- Input Database Coverage: 400328252 bp out of 3545834224 bp ( 11.29 % ) Sampling Time: 02:41:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22838661 Comparison Time: 16:46:26 (hh:mm:ss) Elapsed Time, 230156 HSPs Collected Number of families returned by RECON: 25032 Round Time: 19:44:02 (hh:mm:ss) Elapsed Time : 359 families discovered. RepeatScout/RECON discovery complete: 853 families found Classification Time: 00:37:21 (hh:mm:ss) Elapsed Time Program Time: 28:39:32 (hh:mm:ss) Elapsed Time