RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.RdNCi6/RM_2383.SatJun291700222024 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: 1719705620 Database = /dev/shm/rModeler.RdNCi6/GCA_009762535.1_fNotCel1.pri - Sequences = 468 - Bases = 846760650 - N50 = 37353604 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 39550900-42375795 | [ 5 ] 36726005-39550899 | [ 6 ] 33901111-36726005 | [ 4 ] 31076216-33901110 | [ 4 ] 28251321-31076215 | [ 3 ] 25426427-28251321 | [ 1 ] 22601532-25426426 | [ ] 19776637-22601531 | [ ] 16951743-19776637 | [ ] 14126848-16951742 | [ ] 11301953-14126847 | [ 1 ] 8477059-11301953 | [ ] 5652164-8477058 | [ ] 2827269-5652163 | [ ] 2375-2827269 |************************************************* [ 444 ] Storage Throughput = excellent ( 1016.36 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40949447 bp ( 40014041 non ambiguous ) - Num Contigs Represented = 65 - Sequence extraction : 00:00:47 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:21 (hh:mm:ss) Elapsed Time Round Time: 00:25:54 (hh:mm:ss) Elapsed Time : 538 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10602 repeats masked totaling 2349371 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10180103 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 10033809 bp After Masking: 7234879 bp Masked: 27.89 % -- Input Database Coverage: 10180103 bp out of 846760650 bp ( 1.20 % ) Sampling Time: 00:01:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33670 Comparison Time: 00:05:17 (hh:mm:ss) Elapsed Time, 5747 HSPs Collected Number of families returned by RECON: 1129 Round Time: 00:06:53 (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 : 00:00:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32633 repeats masked totaling 7112603 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30809350 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 30020238 bp After Masking: 21569885 bp Masked: 28.15 % -- Input Database Coverage: 40989453 bp out of 846760650 bp ( 4.84 % ) Sampling Time: 00:03:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 301476 Comparison Time: 00:29:23 (hh:mm:ss) Elapsed Time, 41295 HSPs Collected Number of families returned by RECON: 4294 Round Time: 00:34:28 (hh:mm:ss) Elapsed Time : 103 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 109255 repeats masked totaling 23098187 bp(s). - TE Masking time 00:02:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91374263 bp Num Contigs Represented = 87 Non ambiguous bp: Initial: 90019157 bp After Masking: 62887667 bp Masked: 30.14 % -- Input Database Coverage: 132363716 bp out of 846760650 bp ( 15.63 % ) Sampling Time: 00:11:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2659971 Comparison Time: 03:28:23 (hh:mm:ss) Elapsed Time, 210616 HSPs Collected Number of families returned by RECON: 14165 Round Time: 03:50:07 (hh:mm:ss) Elapsed Time : 473 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 393280 repeats masked totaling 81713537 bp(s). - TE Masking time 00:11:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 274892378 bp Num Contigs Represented = 219 Non ambiguous bp: Initial: 270016046 bp After Masking: 176041059 bp Masked: 34.80 % -- Input Database Coverage: 407256094 bp out of 846760650 bp ( 48.10 % ) Sampling Time: 00:40:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24210361 Comparison Time: 26:05:28 (hh:mm:ss) Elapsed Time, 557374 HSPs Collected Number of families returned by RECON: 52844 Round Time: 28:05:53 (hh:mm:ss) Elapsed Time : 1007 families discovered. RepeatScout/RECON discovery complete: 2134 families found Classification Time: 01:23:29 (hh:mm:ss) Elapsed Time Program Time: 34:26:44 (hh:mm:ss) Elapsed Time