RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ROFR9h/RM_11146.SatDec20437242023 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: 1701520643 Database = /dev/shm/rModeler.ROFR9h/GCA_030035715.1_rRhiFlo1.hap1 - Sequences = 623 - Bases = 2321796813 - N50 = 212296042 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 302342273-323937510 | [ 1 ] 280747036-302342272 | [ ] 259151800-280747036 | [ ] 237556563-259151799 | [ 1 ] 215961326-237556562 | [ 1 ] 194366090-215961326 | [ 2 ] 172770853-194366089 | [ 1 ] 151175616-172770852 | [ 2 ] 129580380-151175616 | [ 1 ] 107985143-129580379 | [ 1 ] 86389906-107985142 | [ 1 ] 64794670-86389906 | [ 1 ] 43199433-64794669 | [ 1 ] 21604196-43199432 | [ 3 ] 8960-21604196 |************************************************** [ 607 ] Storage Throughput = excellent ( 1145.97 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40145065 bp ( 40015388 non ambiguous ) - Num Contigs Represented = 28 - Sequence extraction : 00:04:00 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:09 (hh:mm:ss) Elapsed Time Round Time: 00:28:49 (hh:mm:ss) Elapsed Time : 564 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19715 repeats masked totaling 4413919 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10085228 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10001461 bp After Masking: 5461591 bp Masked: 45.39 % -- Input Database Coverage: 10085228 bp out of 2321796813 bp ( 0.43 % ) Sampling Time: 00:01:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:11 (hh:mm:ss) Elapsed Time, 7710 HSPs Collected Number of families returned by RECON: 1337 Round Time: 00:07:11 (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 : 00:03:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 61339 repeats masked totaling 13902367 bp(s). - TE Masking time 00:00:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30059757 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 30013847 bp After Masking: 15459527 bp Masked: 48.49 % -- Input Database Coverage: 40144985 bp out of 2321796813 bp ( 1.73 % ) Sampling Time: 00:05:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:23:35 (hh:mm:ss) Elapsed Time, 52682 HSPs Collected Number of families returned by RECON: 4034 Round Time: 00:30:40 (hh:mm:ss) Elapsed Time : 147 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:08:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 195659 repeats masked totaling 44791143 bp(s). - TE Masking time 00:02:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90175532 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 90025313 bp After Masking: 43748168 bp Masked: 51.40 % -- Input Database Coverage: 130320517 bp out of 2321796813 bp ( 5.61 % ) Sampling Time: 00:15:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2566245 Comparison Time: 02:26:00 (hh:mm:ss) Elapsed Time, 202150 HSPs Collected Number of families returned by RECON: 11864 Round Time: 02:50:37 (hh:mm:ss) Elapsed Time : 411 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:26:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 654111 repeats masked totaling 147166566 bp(s). - TE Masking time 00:12:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270430184 bp Num Contigs Represented = 99 Non ambiguous bp: Initial: 270007159 bp After Masking: 118498317 bp Masked: 56.11 % -- Input Database Coverage: 400750701 bp out of 2321796813 bp ( 17.26 % ) Sampling Time: 00:49:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23069028 Comparison Time: 17:06:57 (hh:mm:ss) Elapsed Time, 514320 HSPs Collected Number of families returned by RECON: 34933 Round Time: 19:02:35 (hh:mm:ss) Elapsed Time : 1029 families discovered. RepeatScout/RECON discovery complete: 2168 families found Classification Time: 01:29:02 (hh:mm:ss) Elapsed Time Program Time: 24:28:55 (hh:mm:ss) Elapsed Time