RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.tLpGue/RM_2644201.FriNov150506252024 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: 1731675985 Database = /scratch/tmp/rModeler.tLpGue/GCA_039906515.1_mPseCra1.hap1 - Sequences = 439 - Bases = 2674608476 - N50 = 116585307 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 185495619-198744646 | [ 2 ] 172246592-185495618 | [ 1 ] 158997566-172246592 | [ ] 145748539-158997565 | [ 2 ] 132499513-145748539 | [ 2 ] 119250486-132499512 | [ ] 106001459-119250485 | [ 5 ] 92752433-106001459 | [ 2 ] 79503406-92752432 | [ 5 ] 66254380-79503406 | [ ] 53005353-66254379 | [ 2 ] 39756326-53005352 | [ ] 26507300-39756326 | [ 1 ] 13258273-26507299 | [ 1 ] 9247-13258273 |************************************************** [ 416 ] Storage Throughput = excellent ( 1613.27 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40078687 bp ( 40038687 non ambiguous ) - Num Contigs Represented = 77 - Sequence extraction : 00:01:07 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:42 (hh:mm:ss) Elapsed Time Round Time: 00:21:12 (hh:mm:ss) Elapsed Time : 196 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9445 repeats masked totaling 2716616 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10077478 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 10037478 bp After Masking: 7234842 bp Masked: 27.92 % -- Input Database Coverage: 10077478 bp out of 2674608476 bp ( 0.38 % ) Sampling Time: 00:00:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:03:17 (hh:mm:ss) Elapsed Time, 173908 HSPs Collected Number of families returned by RECON: 876 Round Time: 00:05:17 (hh:mm:ss) Elapsed Time : 26 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34844 repeats masked totaling 10681226 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001129 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 30001129 bp After Masking: 18593751 bp Masked: 38.02 % -- Input Database Coverage: 40078607 bp out of 2674608476 bp ( 1.50 % ) Sampling Time: 00:02:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:10:54 (hh:mm:ss) Elapsed Time, 39575 HSPs Collected Number of families returned by RECON: 2180 Round Time: 00:13:26 (hh:mm:ss) Elapsed Time : 69 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 112326 repeats masked totaling 33905430 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90052700 bp Num Contigs Represented = 115 Non ambiguous bp: Initial: 90021640 bp After Masking: 54360641 bp Masked: 39.61 % -- Input Database Coverage: 130131307 bp out of 2674608476 bp ( 4.87 % ) Sampling Time: 00:05:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 01:04:25 (hh:mm:ss) Elapsed Time, 385184 HSPs Collected Number of families returned by RECON: 7256 Round Time: 01:11:37 (hh:mm:ss) Elapsed Time : 170 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 378335 repeats masked totaling 109419748 bp(s). - TE Masking time 00:01:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270195211 bp Num Contigs Represented = 198 Non ambiguous bp: Initial: 270028775 bp After Masking: 156295555 bp Masked: 42.12 % -- Input Database Coverage: 400326518 bp out of 2674608476 bp ( 14.97 % ) Sampling Time: 00:16:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22960476 Comparison Time: 07:19:52 (hh:mm:ss) Elapsed Time, 1845172 HSPs Collected Number of families returned by RECON: 29086 Round Time: 07:51:30 (hh:mm:ss) Elapsed Time : 318 families discovered. RepeatScout/RECON discovery complete: 779 families found Classification Time: 00:15:15 (hh:mm:ss) Elapsed Time Program Time: 09:58:17 (hh:mm:ss) Elapsed Time