RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.8WGzch/RM_29808.SatJul200138472024 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: 1721464722 Database = /dev/shm/rModeler.8WGzch/GCF_016432855.1_SaNama_1.0 - Sequences = 4121 - Bases = 2345513378 - N50 = 45826067 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 91654304-98200354 | [ 1 ] 85108254-91654303 | [ ] 78562204-85108253 | [ 3 ] 72016154-78562203 | [ 1 ] 65470104-72016153 | [ 1 ] 58924054-65470103 | [ 1 ] 52378004-58924053 | [ 5 ] 45831955-52378004 | [ 6 ] 39285905-45831954 | [ 9 ] 32739855-39285904 | [ 8 ] 26193805-32739854 | [ 2 ] 19647755-26193804 | [ 5 ] 13101705-19647754 | [ ] 6555655-13101704 | [ ] 9606-6555655 |************************************************** [ 4079 ] Storage Throughput = excellent ( 1021.29 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40013289 bp ( 40007889 non ambiguous ) - Num Contigs Represented = 219 - Sequence extraction : 00:00:58 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:44 (hh:mm:ss) Elapsed Time Round Time: 00:39:35 (hh:mm:ss) Elapsed Time : 911 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14208 repeats masked totaling 3996285 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004743 bp Num Contigs Represented = 85 Non ambiguous bp: Initial: 10003443 bp After Masking: 4290108 bp Masked: 57.11 % -- Input Database Coverage: 10004743 bp out of 2345513378 bp ( 0.43 % ) Sampling Time: 00:03:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33670 Comparison Time: 00:17:55 (hh:mm:ss) Elapsed Time, 4408 HSPs Collected Number of families returned by RECON: 1049 Round Time: 00:21:50 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44330 repeats masked totaling 12377214 bp(s). - TE Masking time 00:00:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30008466 bp Num Contigs Represented = 180 Non ambiguous bp: Initial: 30004366 bp After Masking: 12306047 bp Masked: 58.99 % -- Input Database Coverage: 40013209 bp out of 2345513378 bp ( 1.71 % ) Sampling Time: 00:11:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 299151 Comparison Time: 01:00:57 (hh:mm:ss) Elapsed Time, 31942 HSPs Collected Number of families returned by RECON: 3411 Round Time: 01:15:00 (hh:mm:ss) Elapsed Time : 84 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:28:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 134916 repeats masked totaling 37002188 bp(s). - TE Masking time 00:02:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90019389 bp Num Contigs Represented = 446 Non ambiguous bp: Initial: 90004849 bp After Masking: 36824731 bp Masked: 59.09 % -- Input Database Coverage: 130032598 bp out of 2345513378 bp ( 5.54 % ) Sampling Time: 00:33:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2706301 Comparison Time: 03:27:20 (hh:mm:ss) Elapsed Time, 257032 HSPs Collected Number of families returned by RECON: 10513 Round Time: 04:17:29 (hh:mm:ss) Elapsed Time : 475 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:19:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 463246 repeats masked totaling 124730971 bp(s). - TE Masking time 00:12:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270069412 bp Num Contigs Represented = 1033 Non ambiguous bp: Initial: 270031113 bp After Masking: 97495468 bp Masked: 63.89 % -- Input Database Coverage: 400102010 bp out of 2345513378 bp ( 17.06 % ) Sampling Time: 01:39:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24405591 Comparison Time: 17:41:05 (hh:mm:ss) Elapsed Time, 716387 HSPs Collected Number of families returned by RECON: 33763 Round Time: 20:19:25 (hh:mm:ss) Elapsed Time : 1062 families discovered. RepeatScout/RECON discovery complete: 2535 families found Classification Time: 01:54:17 (hh:mm:ss) Elapsed Time Program Time: 28:47:36 (hh:mm:ss) Elapsed Time