RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.riotfl/RM_1636323.SunMar311630362024 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: 1711927836 Database = /dev/shm/rModeler.riotfl/GCF_000001405.40_GRCh38.p14 - Sequences = 705 - Bases = 3298430636 - N50 = 156040895 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 232359391-248956422 | [ 2 ] 215762361-232359391 | [ ] 199165331-215762361 | [ ] 182568301-199165331 | [ 2 ] 165971271-182568301 | [ 2 ] 149374241-165971271 | [ 2 ] 132777211-149374241 | [ 5 ] 116180180-132777210 | [ ] 99583150-116180180 | [ 3 ] 82986120-99583150 | [ 2 ] 66389090-82986120 | [ 1 ] 49792060-66389090 | [ 4 ] 33195030-49792060 | [ 1 ] 16598000-33195030 | [ ] 970-16598000 |************************************************** [ 681 ] Storage Throughput = good ( 844.57 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 41890015 bp ( 40007678 non ambiguous ) - Num Contigs Represented = 89 - Sequence extraction : 00:03:36 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:13 (hh:mm:ss) Elapsed Time Round Time: 00:24:35 (hh:mm:ss) Elapsed Time : 263 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13976 repeats masked totaling 2939295 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10662881 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 10002575 bp After Masking: 6617041 bp Masked: 33.85 % -- Input Database Coverage: 10662881 bp out of 3298430636 bp ( 0.32 % ) Sampling Time: 00:01:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 35511 Comparison Time: 00:05:35 (hh:mm:ss) Elapsed Time, 6150 HSPs Collected Number of families returned by RECON: 889 Round Time: 00:07:58 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 45938 repeats masked totaling 9699232 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 31227054 bp Num Contigs Represented = 77 Non ambiguous bp: Initial: 30005023 bp After Masking: 19075180 bp Masked: 36.43 % -- Input Database Coverage: 41889935 bp out of 3298430636 bp ( 1.27 % ) Sampling Time: 00:04:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 306936 Comparison Time: 00:26:25 (hh:mm:ss) Elapsed Time, 30739 HSPs Collected Number of families returned by RECON: 2596 Round Time: 00:32:07 (hh:mm:ss) Elapsed Time : 73 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 144910 repeats masked totaling 31457706 bp(s). - TE Masking time 00:01:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 94666535 bp Num Contigs Represented = 125 Non ambiguous bp: Initial: 90038054 bp After Masking: 55366328 bp Masked: 38.51 % -- Input Database Coverage: 136556470 bp out of 3298430636 bp ( 4.14 % ) Sampling Time: 00:13:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2831010 Comparison Time: 02:49:38 (hh:mm:ss) Elapsed Time, 100311 HSPs Collected Number of families returned by RECON: 9033 Round Time: 03:07:08 (hh:mm:ss) Elapsed Time : 200 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:21:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 478405 repeats masked totaling 102196257 bp(s). - TE Masking time 00:05:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 283935839 bp Num Contigs Represented = 278 Non ambiguous bp: Initial: 270017863 bp After Masking: 157477954 bp Masked: 41.68 % -- Input Database Coverage: 420492309 bp out of 3298430636 bp ( 12.75 % ) Sampling Time: 00:41:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 25443411 Comparison Time: 20:53:18 (hh:mm:ss) Elapsed Time, 437411 HSPs Collected Number of families returned by RECON: 33625 Round Time: 21:56:51 (hh:mm:ss) Elapsed Time : 380 families discovered. RepeatScout/RECON discovery complete: 934 families found Classification Time: 00:40:01 (hh:mm:ss) Elapsed Time Program Time: 26:48:40 (hh:mm:ss) Elapsed Time