RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.WeV2HR/RM_9549.FriJul122014562024 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: 1720840494 Database = /dev/shm/rModeler.WeV2HR/GCF_002922805.2_ASM292280v2 - Sequences = 8493 - Bases = 778703520 - N50 = 31267959 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 34736863-37217997 | [ 3 ] 32255730-34736863 | [ 5 ] 29774597-32255730 | [ 4 ] 27293464-29774597 | [ 5 ] 24812331-27293464 | [ 4 ] 22331198-24812331 | [ 2 ] 19850065-22331198 | [ 1 ] 17368931-19850064 | [ ] 14887798-17368931 | [ ] 12406665-14887798 | [ ] 9925532-12406665 | [ ] 7444399-9925532 | [ ] 4963266-7444399 | [ ] 2482133-4963266 | [ ] 1000-2482133 |************************************************** [ 8469 ] Storage Throughput = excellent ( 1031.48 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 42015909 bp ( 40005462 non ambiguous ) - Num Contigs Represented = 490 - Sequence extraction : 00:00:42 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:02 (hh:mm:ss) Elapsed Time Round Time: 00:25:14 (hh:mm:ss) Elapsed Time : 741 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20526 repeats masked totaling 2593240 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10546371 bp Num Contigs Represented = 176 Non ambiguous bp: Initial: 10026746 bp After Masking: 7264949 bp Masked: 27.54 % -- Input Database Coverage: 10546371 bp out of 778703520 bp ( 1.35 % ) Sampling Time: 00:00:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 74691 Comparison Time: 00:08:26 (hh:mm:ss) Elapsed Time, 9786 HSPs Collected Number of families returned by RECON: 1305 Round Time: 00:09:45 (hh:mm:ss) Elapsed Time : 25 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 63441 repeats masked totaling 8077364 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 31519974 bp Num Contigs Represented = 341 Non ambiguous bp: Initial: 30019748 bp After Masking: 21377822 bp Masked: 28.79 % -- Input Database Coverage: 42066345 bp out of 778703520 bp ( 5.40 % ) Sampling Time: 00:02:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 551775 Comparison Time: 00:40:23 (hh:mm:ss) Elapsed Time, 52139 HSPs Collected Number of families returned by RECON: 3875 Round Time: 00:45:12 (hh:mm:ss) Elapsed Time : 134 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 203152 repeats masked totaling 26879326 bp(s). - TE Masking time 00:02:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 95378067 bp Num Contigs Represented = 1116 Non ambiguous bp: Initial: 90033645 bp After Masking: 61600632 bp Masked: 31.58 % -- Input Database Coverage: 137444412 bp out of 778703520 bp ( 17.65 % ) Sampling Time: 00:08:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 5456556 Comparison Time: 04:26:48 (hh:mm:ss) Elapsed Time, 205270 HSPs Collected Number of families returned by RECON: 12797 Round Time: 04:44:23 (hh:mm:ss) Elapsed Time : 427 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 665519 repeats masked totaling 90797730 bp(s). - TE Masking time 00:13:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 284647716 bp Num Contigs Represented = 3143 Non ambiguous bp: Initial: 270012627 bp After Masking: 174349546 bp Masked: 35.43 % -- Input Database Coverage: 422092128 bp out of 778703520 bp ( 54.20 % ) Sampling Time: 00:30:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 48280051 Comparison Time: 33:01:23 (hh:mm:ss) Elapsed Time, 532151 HSPs Collected Number of families returned by RECON: 46973 Round Time: 34:40:36 (hh:mm:ss) Elapsed Time : 975 families discovered. RepeatScout/RECON discovery complete: 2302 families found Classification Time: 01:25:12 (hh:mm:ss) Elapsed Time Program Time: 42:10:22 (hh:mm:ss) Elapsed Time