RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.KsM6E6/RM_1320395.SatFeb80718012025 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: 1739027853 Database = /dev/shm/rModeler.KsM6E6/GCA_046255685.1_fAmbSpe1.hap1 - Sequences = 892 - Bases = 817459139 - N50 = 32291948 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 39416975-42231476 | [ 1 ] 36602474-39416974 | [ 3 ] 33787973-36602473 | [ 6 ] 30973472-33787972 | [ 8 ] 28158971-30973471 | [ 2 ] 25344470-28158970 | [ 3 ] 22529969-25344469 | [ ] 19715468-22529968 | [ ] 16900967-19715467 | [ ] 14086466-16900966 | [ ] 11271965-14086465 | [ ] 8457464-11271964 | [ ] 5642963-8457463 | [ ] 2828462-5642962 | [ ] 13962-2828462 |************************************************** [ 869 ] Storage Throughput = excellent ( 1765.99 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40025022 bp ( 40020222 non ambiguous ) - Num Contigs Represented = 127 - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:00 (hh:mm:ss) Elapsed Time Round Time: 01:26:00 (hh:mm:ss) Elapsed Time : 730 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 00:01:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10006 repeats masked totaling 2569305 bp(s). - TE Masking time 00:00:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10034752 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 10034152 bp After Masking: 5735604 bp Masked: 42.84 % -- Input Database Coverage: 10034752 bp out of 817459139 bp ( 1.23 % ) Sampling Time: 00:02:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33411 Comparison Time: 01:59:15 (hh:mm:ss) Elapsed Time, 7019 HSPs Collected Number of families returned by RECON: 1099 Round Time: 02:06:11 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31488 repeats masked totaling 8170571 bp(s). - TE Masking time 00:00:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30030129 bp Num Contigs Represented = 101 Non ambiguous bp: Initial: 30025929 bp After Masking: 17913133 bp Masked: 40.34 % -- Input Database Coverage: 40064881 bp out of 817459139 bp ( 4.90 % ) Sampling Time: 00:04:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 296065 Comparison Time: 05:55:14 (hh:mm:ss) Elapsed Time, 54365 HSPs Collected Number of families returned by RECON: 4240 Round Time: 06:16:20 (hh:mm:ss) Elapsed Time : 111 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 100672 repeats masked totaling 26048055 bp(s). - TE Masking time 00:01:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90044809 bp Num Contigs Represented = 186 Non ambiguous bp: Initial: 90035809 bp After Masking: 50333334 bp Masked: 44.10 % -- Input Database Coverage: 130109690 bp out of 817459139 bp ( 15.92 % ) Sampling Time: 00:14:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2641551 Comparison Time: 17:48:40 (hh:mm:ss) Elapsed Time, 287515 HSPs Collected Number of families returned by RECON: 12785 Round Time: 19:25:40 (hh:mm:ss) Elapsed Time : 512 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:34:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 359221 repeats masked totaling 94349791 bp(s). - TE Masking time 00:04:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270037552 bp Num Contigs Represented = 439 Non ambiguous bp: Initial: 270005152 bp After Masking: 134303612 bp Masked: 50.26 % -- Input Database Coverage: 400147242 bp out of 817459139 bp ( 48.95 % ) Sampling Time: 00:42:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23670640 Comparison Time: 21:36:20 (hh:mm:ss) Elapsed Time, 823746 HSPs Collected Number of families returned by RECON: 41505 Round Time: 22:39:45 (hh:mm:ss) Elapsed Time : 1033 families discovered. RepeatScout/RECON discovery complete: 2394 families found Classification Time: 00:59:02 (hh:mm:ss) Elapsed Time Program Time: 52:52:58 (hh:mm:ss) Elapsed Time