RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.6XqEbY/RM_24441.ThuDec70344062023 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: 1701949444 Database = /dev/shm/rModeler.6XqEbY/GCA_949748355.1_fMelGel1.1 - Sequences = 534 - Bases = 661975483 - N50 = 28063322 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 31611996-33869925 | [ 3 ] 29354068-31611996 | [ 3 ] 27096140-29354068 | [ 6 ] 24838211-27096139 | [ 4 ] 22580283-24838211 | [ 3 ] 20322355-22580283 | [ 2 ] 18064426-20322354 | [ 1 ] 15806498-18064426 | [ 1 ] 13548570-15806498 | [ ] 11290641-13548569 | [ 1 ] 9032713-11290641 | [ ] 6774785-9032713 | [ ] 4516856-6774784 | [ ] 2258928-4516856 | [ ] 1000-2258928 |************************************************** [ 510 ] Storage Throughput = excellent ( 1052.48 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40020924 bp ( 40013924 non ambiguous ) - Num Contigs Represented = 84 - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:50 (hh:mm:ss) Elapsed Time Round Time: 00:29:57 (hh:mm:ss) Elapsed Time : 511 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 00:08:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7015 repeats masked totaling 1628533 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027728 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10025928 bp After Masking: 7273572 bp Masked: 27.45 % -- Input Database Coverage: 10027728 bp out of 661975483 bp ( 1.51 % ) Sampling Time: 00:09:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:55 (hh:mm:ss) Elapsed Time, 22990 HSPs Collected Number of families returned by RECON: 1166 Round Time: 00:16:42 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22206 repeats masked totaling 4897899 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30033171 bp Num Contigs Represented = 75 Non ambiguous bp: Initial: 30027971 bp After Masking: 21546476 bp Masked: 28.25 % -- Input Database Coverage: 40060899 bp out of 661975483 bp ( 6.05 % ) Sampling Time: 00:15:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 291466 Comparison Time: 00:33:04 (hh:mm:ss) Elapsed Time, 47057 HSPs Collected Number of families returned by RECON: 4533 Round Time: 00:49:48 (hh:mm:ss) Elapsed Time : 97 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:41:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 74259 repeats masked totaling 15767829 bp(s). - TE Masking time 00:02:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90017698 bp Num Contigs Represented = 144 Non ambiguous bp: Initial: 90000990 bp After Masking: 64468761 bp Masked: 28.37 % -- Input Database Coverage: 130078597 bp out of 661975483 bp ( 19.65 % ) Sampling Time: 00:44:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2604903 Comparison Time: 03:19:26 (hh:mm:ss) Elapsed Time, 252551 HSPs Collected Number of families returned by RECON: 16810 Round Time: 04:15:57 (hh:mm:ss) Elapsed Time : 387 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 02:10:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 277101 repeats masked totaling 58028635 bp(s). - TE Masking time 00:10:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270086703 bp Num Contigs Represented = 323 Non ambiguous bp: Initial: 270039011 bp After Masking: 182176787 bp Masked: 32.54 % -- Input Database Coverage: 400165300 bp out of 661975483 bp ( 60.45 % ) Sampling Time: 02:24:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23540091 Comparison Time: 25:18:25 (hh:mm:ss) Elapsed Time, 1023025 HSPs Collected Number of families returned by RECON: 63700 Round Time: 29:37:59 (hh:mm:ss) Elapsed Time : 979 families discovered. RepeatScout/RECON discovery complete: 1991 families found Classification Time: 01:41:34 (hh:mm:ss) Elapsed Time Program Time: 37:11:57 (hh:mm:ss) Elapsed Time