RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.WDPpPs/RM_1960729.WedJul162053502025 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: 1752724429 Database = /dev/shm/rModeler.WDPpPs/GCA_029633875.2_fHopMal1.hap2 - Sequences = 451 - Bases = 1026599506 - N50 = 48956927 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 84972061-91041448 | [ 2 ] 78902675-84972061 | [ 1 ] 72833288-78902674 | [ 1 ] 66763902-72833288 | [ ] 60694516-66763902 | [ 1 ] 54625129-60694515 | [ 1 ] 48555743-54625129 | [ 1 ] 42486356-48555742 | [ 4 ] 36416970-42486356 | [ 5 ] 30347584-36416970 | [ 2 ] 24278197-30347583 | [ ] 18208811-24278197 | [ ] 12139424-18208810 | [ ] 6070038-12139424 | [ ] 652-6070038 |************************************************** [ 433 ] Storage Throughput = excellent ( 1139.20 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 41729453 bp ( 40017901 non ambiguous ) - Num Contigs Represented = 81 - Sequence extraction : 00:01:16 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:30:27 (hh:mm:ss) Elapsed Time Round Time: 00:41:35 (hh:mm:ss) Elapsed Time : 576 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16130 repeats masked totaling 2423015 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10545111 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10005565 bp After Masking: 6488353 bp Masked: 35.15 % -- Input Database Coverage: 10545111 bp out of 1026599506 bp ( 1.03 % ) Sampling Time: 00:02:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 35245 Comparison Time: 00:06:35 (hh:mm:ss) Elapsed Time, 206554 HSPs Collected Number of families returned by RECON: 1488 Round Time: 00:13:13 (hh:mm:ss) Elapsed Time : 23 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46357 repeats masked totaling 7337895 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 31184262 bp Num Contigs Represented = 71 Non ambiguous bp: Initial: 30012256 bp After Masking: 19190329 bp Masked: 36.06 % -- Input Database Coverage: 41729373 bp out of 1026599506 bp ( 4.06 % ) Sampling Time: 00:06:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 310078 Comparison Time: 00:29:59 (hh:mm:ss) Elapsed Time, 138715 HSPs Collected Number of families returned by RECON: 4696 Round Time: 00:38:37 (hh:mm:ss) Elapsed Time : 135 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 155695 repeats masked totaling 24398420 bp(s). - TE Masking time 00:02:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 92793444 bp Num Contigs Represented = 116 Non ambiguous bp: Initial: 90033046 bp After Masking: 55550002 bp Masked: 38.30 % -- Input Database Coverage: 134522817 bp out of 1026599506 bp ( 13.10 % ) Sampling Time: 00:20:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2741311 Comparison Time: 03:19:59 (hh:mm:ss) Elapsed Time, 1642563 HSPs Collected Number of families returned by RECON: 14650 Round Time: 03:55:11 (hh:mm:ss) Elapsed Time : 443 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:42:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 553106 repeats masked totaling 90334298 bp(s). - TE Masking time 00:12:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 280663202 bp Num Contigs Represented = 240 Non ambiguous bp: Initial: 270025282 bp After Masking: 151012682 bp Masked: 44.07 % -- Input Database Coverage: 415186019 bp out of 1026599506 bp ( 40.44 % ) Sampling Time: 01:04:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 25038426 Comparison Time: 24:11:13 (hh:mm:ss) Elapsed Time, 1247030 HSPs Collected Number of families returned by RECON: 50056 Round Time: 26:42:36 (hh:mm:ss) Elapsed Time : 1043 families discovered. RepeatScout/RECON discovery complete: 2220 families found Classification Time: 01:42:07 (hh:mm:ss) Elapsed Time Program Time: 33:53:19 (hh:mm:ss) Elapsed Time