RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.8iADaZ/RM_11531.ThuDec72353262023 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: 1702022004 Database = /dev/shm/rModeler.8iADaZ/GCA_949987685.1_fAmmMar1.1 - Sequences = 617 - Bases = 777835610 - N50 = 32613110 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 37092950-39742375 | [ 2 ] 34443525-37092950 | [ 4 ] 31794100-34443525 | [ 6 ] 29144675-31794100 | [ 4 ] 26495250-29144675 | [ 5 ] 23845825-26495250 | [ ] 21196400-23845825 | [ 2 ] 18546975-21196400 | [ ] 15897550-18546975 | [ 1 ] 13248125-15897550 | [ ] 10598700-13248125 | [ ] 7949275-10598700 | [ ] 5299850-7949275 | [ ] 2650425-5299850 | [ 1 ] 1000-2650425 |************************************************** [ 592 ] Storage Throughput = excellent ( 1112.80 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40045087 bp ( 40036063 non ambiguous ) - Num Contigs Represented = 89 - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:34 (hh:mm:ss) Elapsed Time Round Time: 00:55:38 (hh:mm:ss) Elapsed Time : 609 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10743 repeats masked totaling 2474231 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027476 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 10024476 bp After Masking: 6891484 bp Masked: 31.25 % -- Input Database Coverage: 10027476 bp out of 777835610 bp ( 1.29 % ) Sampling Time: 00:01:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:05:30 (hh:mm:ss) Elapsed Time, 13548 HSPs Collected Number of families returned by RECON: 1057 Round Time: 00:07:37 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31904 repeats masked totaling 7339530 bp(s). - TE Masking time 00:01:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30017531 bp Num Contigs Represented = 65 Non ambiguous bp: Initial: 30011507 bp After Masking: 20398620 bp Masked: 32.03 % -- Input Database Coverage: 40045007 bp out of 777835610 bp ( 5.15 % ) Sampling Time: 00:05:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 290703 Comparison Time: 00:28:53 (hh:mm:ss) Elapsed Time, 32510 HSPs Collected Number of families returned by RECON: 3761 Round Time: 00:34:56 (hh:mm:ss) Elapsed Time : 70 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 102143 repeats masked totaling 22693596 bp(s). - TE Masking time 00:03:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90050473 bp Num Contigs Represented = 154 Non ambiguous bp: Initial: 90029986 bp After Masking: 61281730 bp Masked: 31.93 % -- Input Database Coverage: 130095480 bp out of 777835610 bp ( 16.73 % ) Sampling Time: 00:14:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2630071 Comparison Time: 03:20:15 (hh:mm:ss) Elapsed Time, 239044 HSPs Collected Number of families returned by RECON: 13377 Round Time: 03:47:48 (hh:mm:ss) Elapsed Time : 459 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:29:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 358574 repeats masked totaling 80635248 bp(s). - TE Masking time 00:15:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270100917 bp Num Contigs Represented = 317 Non ambiguous bp: Initial: 270032427 bp After Masking: 171174424 bp Masked: 36.61 % -- Input Database Coverage: 400196397 bp out of 777835610 bp ( 51.45 % ) Sampling Time: 00:49:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23588146 Comparison Time: 25:13:05 (hh:mm:ss) Elapsed Time, 728334 HSPs Collected Number of families returned by RECON: 47647 Round Time: 27:20:32 (hh:mm:ss) Elapsed Time : 1126 families discovered. RepeatScout/RECON discovery complete: 2269 families found Classification Time: 01:54:04 (hh:mm:ss) Elapsed Time Program Time: 34:40:35 (hh:mm:ss) Elapsed Time