RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Fu5zj8/RM_1618810.SatApr190614002025 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: 1745068440 Database = /dev/shm/rModeler.Fu5zj8/GCF_030028105.1_sMobBir1.hap1 - Sequences = 4715 - Bases = 4014635230 - N50 = 158616986 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 237366999-254321047 | [ 2 ] 220412952-237366999 | [ 1 ] 203458904-220412951 | [ 2 ] 186504857-203458904 | [ 2 ] 169550809-186504856 | [ 1 ] 152596762-169550809 | [ 1 ] 135642714-152596761 | [ 1 ] 118688667-135642714 | [ ] 101734619-118688666 | [ 3 ] 84780572-101734619 | [ 2 ] 67826524-84780571 | [ 6 ] 50872477-67826524 | [ 6 ] 33918429-50872476 | [ 5 ] 16964382-33918429 | [ 1 ] 10335-16964382 |************************************************** [ 4682 ] Storage Throughput = excellent ( 1701.57 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40257864 bp ( 40006799 non ambiguous ) - Num Contigs Represented = 150 - Sequence extraction : 00:01:23 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:29 (hh:mm:ss) Elapsed Time Round Time: 00:13:42 (hh:mm:ss) Elapsed Time : 667 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19134 repeats masked totaling 5190169 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10107704 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 10012127 bp After Masking: 3394830 bp Masked: 66.09 % -- Input Database Coverage: 10107704 bp out of 4014635230 bp ( 0.25 % ) Sampling Time: 00:02:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:02:34 (hh:mm:ss) Elapsed Time, 4825 HSPs Collected Number of families returned by RECON: 526 Round Time: 00:07:16 (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 : 00:01:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 57972 repeats masked totaling 15986667 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30197437 bp Num Contigs Represented = 122 Non ambiguous bp: Initial: 30041949 bp After Masking: 9938259 bp Masked: 66.92 % -- Input Database Coverage: 40305141 bp out of 4014635230 bp ( 1.00 % ) Sampling Time: 00:06:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 297606 Comparison Time: 00:09:24 (hh:mm:ss) Elapsed Time, 22721 HSPs Collected Number of families returned by RECON: 1758 Round Time: 00:16:58 (hh:mm:ss) Elapsed Time : 61 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 179572 repeats masked totaling 48982936 bp(s). - TE Masking time 00:00:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90836103 bp Num Contigs Represented = 300 Non ambiguous bp: Initial: 90017267 bp After Masking: 28563375 bp Masked: 68.27 % -- Input Database Coverage: 131141244 bp out of 4014635230 bp ( 3.27 % ) Sampling Time: 00:21:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2685403 Comparison Time: 00:44:45 (hh:mm:ss) Elapsed Time, 98929 HSPs Collected Number of families returned by RECON: 4400 Round Time: 01:08:06 (hh:mm:ss) Elapsed Time : 237 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:48:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 575531 repeats masked totaling 156466688 bp(s). - TE Masking time 00:03:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272435786 bp Num Contigs Represented = 717 Non ambiguous bp: Initial: 270017479 bp After Masking: 77430309 bp Masked: 71.32 % -- Input Database Coverage: 403577030 bp out of 4014635230 bp ( 10.05 % ) Sampling Time: 01:01:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24189490 Comparison Time: 04:20:39 (hh:mm:ss) Elapsed Time, 258021 HSPs Collected Number of families returned by RECON: 13210 Round Time: 05:25:52 (hh:mm:ss) Elapsed Time : 479 families discovered. RepeatScout/RECON discovery complete: 1452 families found Classification Time: 00:30:10 (hh:mm:ss) Elapsed Time Program Time: 07:42:04 (hh:mm:ss) Elapsed Time