RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.xw1jGN/RM_52511.SunJan80710222023 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: 1673190621 Database = /dev/shm/rModeler.xw1jGN/GCF_902686445.1_mSciCar1.2 - Sequences = 752 - Bases = 2815397268 - N50 = 154993933 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 195061317-208993527 | [ 2 ] 181129108-195061317 | [ 1 ] 167196899-181129108 | [ 2 ] 153264690-167196899 | [ 2 ] 139332481-153264690 | [ 3 ] 125400271-139332480 | [ 2 ] 111468062-125400271 | [ 1 ] 97535853-111468062 | [ ] 83603644-97535853 | [ 2 ] 69671435-83603644 | [ 1 ] 55739225-69671434 | [ 2 ] 41807016-55739225 | [ ] 27874807-41807016 | [ 2 ] 13942598-27874807 | [ ] 10389-13942598 |************************************************** [ 732 ] Storage Throughput = excellent ( 1310.64 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40013584 bp ( 40003384 non ambiguous ) - Num Contigs Represented = 99 - Sequence extraction : 00:03:24 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:43 (hh:mm:ss) Elapsed Time Round Time: 00:34:33 (hh:mm:ss) Elapsed Time : 227 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10424 repeats masked totaling 2670182 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10033718 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 10030718 bp After Masking: 7236773 bp Masked: 27.85 % -- Input Database Coverage: 10033718 bp out of 2815397268 bp ( 0.36 % ) Sampling Time: 00:01:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:50 (hh:mm:ss) Elapsed Time, 8274 HSPs Collected Number of families returned by RECON: 915 Round Time: 00:07:42 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 35421 repeats masked totaling 8473142 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30019937 bp Num Contigs Represented = 85 Non ambiguous bp: Initial: 30012737 bp After Masking: 21224101 bp Masked: 29.28 % -- Input Database Coverage: 40053655 bp out of 2815397268 bp ( 1.42 % ) Sampling Time: 00:04:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:28:49 (hh:mm:ss) Elapsed Time, 25932 HSPs Collected Number of families returned by RECON: 2426 Round Time: 00:34:01 (hh:mm:ss) Elapsed Time : 51 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 109861 repeats masked totaling 27346232 bp(s). - TE Masking time 00:01:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90063171 bp Num Contigs Represented = 178 Non ambiguous bp: Initial: 90035678 bp After Masking: 61853907 bp Masked: 31.30 % -- Input Database Coverage: 130116826 bp out of 2815397268 bp ( 4.62 % ) Sampling Time: 00:12:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 03:09:41 (hh:mm:ss) Elapsed Time, 141488 HSPs Collected Number of families returned by RECON: 8604 Round Time: 03:27:16 (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 : 00:25:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 375683 repeats masked totaling 90575153 bp(s). - TE Masking time 00:07:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270055145 bp Num Contigs Represented = 275 Non ambiguous bp: Initial: 270005701 bp After Masking: 176926237 bp Masked: 34.47 % -- Input Database Coverage: 400171971 bp out of 2815397268 bp ( 14.21 % ) Sampling Time: 00:43:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23007936 Comparison Time: 22:47:48 (hh:mm:ss) Elapsed Time, 486377 HSPs Collected Number of families returned by RECON: 35862 Round Time: 24:06:58 (hh:mm:ss) Elapsed Time : 446 families discovered. RepeatScout/RECON discovery complete: 919 families found Classification Time: 01:08:28 (hh:mm:ss) Elapsed Time Program Time: 29:58:58 (hh:mm:ss) Elapsed Time