RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.TEKBI1/RM_233517.SunMar310343522024 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: 1711881832 Database = /dev/shm/rModeler.TEKBI1/GCA_963930695.1_fLabBer1.1 - Sequences = 132 - Bases = 720227340 - N50 = 31292968 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 35473738-38007505 |* [ 3 ] 32939971-35473738 |** [ 5 ] 30406204-32939971 |** [ 5 ] 27872437-30406204 | [ 2 ] 25338670-27872437 |* [ 4 ] 22804903-25338670 |* [ 3 ] 20271136-22804903 | [ 1 ] 17737369-20271136 | [ ] 15203602-17737369 | [ ] 12669835-15203602 | [ 1 ] 10136068-12669835 | [ ] 7602301-10136068 | [ ] 5068534-7602301 | [ ] 2534767-5068534 | [ ] 1000-2534767 |************************************************** [ 108 ] Storage Throughput = excellent ( 1422.10 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40022739 bp ( 40014506 non ambiguous ) - Num Contigs Represented = 36 - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:50 (hh:mm:ss) Elapsed Time Round Time: 00:22:22 (hh:mm:ss) Elapsed Time : 463 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 00:01:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8092 repeats masked totaling 1411679 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10031873 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10030040 bp After Masking: 7894822 bp Masked: 21.29 % -- Input Database Coverage: 10031873 bp out of 720227340 bp ( 1.39 % ) Sampling Time: 00:02:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:09 (hh:mm:ss) Elapsed Time, 5977 HSPs Collected Number of families returned by RECON: 1216 Round Time: 00:08:31 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23201 repeats masked totaling 4218560 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30030831 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 30024431 bp After Masking: 23577083 bp Masked: 21.47 % -- Input Database Coverage: 40062704 bp out of 720227340 bp ( 5.56 % ) Sampling Time: 00:06:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:30:12 (hh:mm:ss) Elapsed Time, 46313 HSPs Collected Number of families returned by RECON: 4130 Round Time: 00:37:29 (hh:mm:ss) Elapsed Time : 101 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 82078 repeats masked totaling 14356995 bp(s). - TE Masking time 00:01:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90034525 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 90014358 bp After Masking: 69873599 bp Masked: 22.38 % -- Input Database Coverage: 130097229 bp out of 720227340 bp ( 18.06 % ) Sampling Time: 00:18:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 03:20:42 (hh:mm:ss) Elapsed Time, 340393 HSPs Collected Number of families returned by RECON: 15460 Round Time: 03:48:17 (hh:mm:ss) Elapsed Time : 440 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:46:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 306800 repeats masked totaling 54050134 bp(s). - TE Masking time 00:08:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270091564 bp Num Contigs Represented = 72 Non ambiguous bp: Initial: 270028564 bp After Masking: 199179271 bp Masked: 26.24 % -- Input Database Coverage: 400188793 bp out of 720227340 bp ( 55.56 % ) Sampling Time: 00:58:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22940151 Comparison Time: 24:50:28 (hh:mm:ss) Elapsed Time, 1622189 HSPs Collected Number of families returned by RECON: 60760 Round Time: 27:03:53 (hh:mm:ss) Elapsed Time : 1061 families discovered. RepeatScout/RECON discovery complete: 2078 families found Classification Time: 01:37:01 (hh:mm:ss) Elapsed Time Program Time: 33:37:33 (hh:mm:ss) Elapsed Time