RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.hdYNvz/RM_1295496.FriMar220209362024 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: 1711098575 Database = /dev/shm/rModeler.hdYNvz/GCA_036417665.1_bPasDom1.hap1 - Sequences = 334 - Bases = 1310114252 - N50 = 84378497 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 150346880-161085800 | [ 1 ] 139607960-150346880 | [ ] 128869040-139607960 | [ ] 118130120-128869040 | [ 2 ] 107391200-118130120 | [ ] 96652280-107391200 | [ ] 85913360-96652280 | [ ] 75174440-85913360 | [ 3 ] 64435520-75174440 | [ 1 ] 53696600-64435520 | [ 2 ] 42957680-53696600 | [ 3 ] 32218760-42957680 | [ 1 ] 21479840-32218760 | [ 1 ] 10740920-21479840 |* [ 8 ] 2000-10740920 |************************************************** [ 312 ] Storage Throughput = excellent ( 1376.52 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40034237 bp ( 40032437 non ambiguous ) - Num Contigs Represented = 78 - Sequence extraction : 00:01:31 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:14 (hh:mm:ss) Elapsed Time Round Time: 00:26:52 (hh:mm:ss) Elapsed Time : 179 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3191 repeats masked totaling 1238343 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10037514 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 10037314 bp After Masking: 7515501 bp Masked: 25.12 % -- Input Database Coverage: 10037514 bp out of 1310114252 bp ( 0.77 % ) Sampling Time: 00:03:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:11:19 (hh:mm:ss) Elapsed Time, 446684 HSPs Collected Number of families returned by RECON: 291 Round Time: 00:15:25 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9333 repeats masked totaling 3400192 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30036831 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 30035231 bp After Masking: 23292485 bp Masked: 22.45 % -- Input Database Coverage: 40074345 bp out of 1310114252 bp ( 3.06 % ) Sampling Time: 00:06:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:45:14 (hh:mm:ss) Elapsed Time, 1366031 HSPs Collected Number of families returned by RECON: 1519 Round Time: 00:52:58 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 27993 repeats masked totaling 9067451 bp(s). - TE Masking time 00:01:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90038979 bp Num Contigs Represented = 102 Non ambiguous bp: Initial: 90036179 bp After Masking: 71285187 bp Masked: 20.83 % -- Input Database Coverage: 130113324 bp out of 1310114252 bp ( 9.93 % ) Sampling Time: 00:20:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2570778 Comparison Time: 06:00:43 (hh:mm:ss) Elapsed Time, 23373667 HSPs Collected Number of families returned by RECON: 8724 Round Time: 06:32:51 (hh:mm:ss) Elapsed Time : 93 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:37:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 94452 repeats masked totaling 34005559 bp(s). - TE Masking time 00:06:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270025277 bp Num Contigs Represented = 171 Non ambiguous bp: Initial: 270016077 bp After Masking: 210625001 bp Masked: 22.00 % -- Input Database Coverage: 400138601 bp out of 1310114252 bp ( 30.54 % ) Sampling Time: 00:55:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23007936 Comparison Time: 48:13:51 (hh:mm:ss) Elapsed Time, 209787176 HSPs Collected Number of families returned by RECON: 56050 Round Time: 53:10:32 (hh:mm:ss) Elapsed Time : 358 families discovered. RepeatScout/RECON discovery complete: 644 families found Classification Time: 01:03:42 (hh:mm:ss) Elapsed Time Program Time: 62:22:20 (hh:mm:ss) Elapsed Time