RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.s9uldY/RM_4028942.WedJul101439052024 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: 1720647544 Database = /dev/shm/rModeler.s9uldY/GCF_029448725.1_ASM2944872v1 - Sequences = 2721 - Bases = 2496185110 - N50 = 51265593 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 94562328-101316066 | [ 2 ] 87808591-94562328 | [ 1 ] 81054853-87808590 | [ 1 ] 74301116-81054853 | [ 1 ] 67547378-74301115 | [ 1 ] 60793641-67547378 | [ 3 ] 54039903-60793640 | [ 5 ] 47286166-54039903 | [ 11 ] 40532428-47286165 | [ 9 ] 33778691-40532428 | [ 4 ] 27024953-33778690 | [ 2 ] 20271216-27024953 | [ 2 ] 13517478-20271215 | [ ] 6763741-13517478 | [ ] 10004-6763741 |************************************************** [ 2679 ] Storage Throughput = good ( 985.07 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40064307 bp ( 40022274 non ambiguous ) - Num Contigs Represented = 177 - Sequence extraction : 00:01:09 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:21 (hh:mm:ss) Elapsed Time Round Time: 00:32:31 (hh:mm:ss) Elapsed Time : 784 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11943 repeats masked totaling 3385024 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10037416 bp Num Contigs Represented = 86 Non ambiguous bp: Initial: 10026561 bp After Masking: 3586393 bp Masked: 64.23 % -- Input Database Coverage: 10037416 bp out of 2496185110 bp ( 0.40 % ) Sampling Time: 00:06:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:04:53 (hh:mm:ss) Elapsed Time, 4714 HSPs Collected Number of families returned by RECON: 925 Round Time: 00:11:54 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 38931 repeats masked totaling 11164738 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30059188 bp Num Contigs Represented = 131 Non ambiguous bp: Initial: 30028010 bp After Masking: 11973158 bp Masked: 60.13 % -- Input Database Coverage: 40096604 bp out of 2496185110 bp ( 1.61 % ) Sampling Time: 00:16:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 294528 Comparison Time: 00:21:46 (hh:mm:ss) Elapsed Time, 35268 HSPs Collected Number of families returned by RECON: 3398 Round Time: 00:39:01 (hh:mm:ss) Elapsed Time : 93 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:49:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 120437 repeats masked totaling 33981877 bp(s). - TE Masking time 00:01:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90156164 bp Num Contigs Represented = 276 Non ambiguous bp: Initial: 90007596 bp After Masking: 33886596 bp Masked: 62.35 % -- Input Database Coverage: 130252768 bp out of 2496185110 bp ( 5.22 % ) Sampling Time: 00:53:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2639253 Comparison Time: 01:52:42 (hh:mm:ss) Elapsed Time, 240037 HSPs Collected Number of families returned by RECON: 9986 Round Time: 02:52:43 (hh:mm:ss) Elapsed Time : 484 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 02:34:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 404965 repeats masked totaling 111511382 bp(s). - TE Masking time 00:07:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270467878 bp Num Contigs Represented = 678 Non ambiguous bp: Initial: 270014709 bp After Masking: 91074730 bp Masked: 66.27 % -- Input Database Coverage: 400720646 bp out of 2496185110 bp ( 16.05 % ) Sampling Time: 02:49:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23836060 Comparison Time: 11:20:01 (hh:mm:ss) Elapsed Time, 618642 HSPs Collected Number of families returned by RECON: 31819 Round Time: 15:33:51 (hh:mm:ss) Elapsed Time : 976 families discovered. RepeatScout/RECON discovery complete: 2338 families found Classification Time: 01:28:37 (hh:mm:ss) Elapsed Time Program Time: 21:18:37 (hh:mm:ss) Elapsed Time