RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.vImCOQ/RM_2397629.WedDec42130592024 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: 1733376659 Database = /scratch/tmp/rModeler.vImCOQ/GCA_964214025.1_sMusAst1.hap2.1 - Sequences = 4403 - Bases = 3476679425 - N50 = 112673543 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 189134175-202643688 | [ 1 ] 175624662-189134174 | [ ] 162115150-175624662 | [ 1 ] 148605637-162115149 | [ 4 ] 135096125-148605637 | [ 3 ] 121586612-135096124 | [ 1 ] 108077100-121586612 | [ 3 ] 94567587-108077099 | [ 3 ] 81058075-94567587 | [ 5 ] 67548562-81058074 | [ 2 ] 54039050-67548562 | [ 2 ] 40529537-54039049 | [ 2 ] 27020025-40529537 | [ 1 ] 13510512-27020024 | [ 2 ] 1000-13510512 |************************************************** [ 4373 ] Storage Throughput = excellent ( 1452.84 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40026454 bp ( 40017254 non ambiguous ) - Num Contigs Represented = 158 - Sequence extraction : 00:01:04 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:39 (hh:mm:ss) Elapsed Time Round Time: 00:12:26 (hh:mm:ss) Elapsed Time : 507 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 00:02:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21400 repeats masked totaling 4984040 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10006348 bp Num Contigs Represented = 59 Non ambiguous bp: Initial: 10004148 bp After Masking: 3995045 bp Masked: 60.07 % -- Input Database Coverage: 10006348 bp out of 3476679425 bp ( 0.29 % ) Sampling Time: 00:02:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:02:35 (hh:mm:ss) Elapsed Time, 6868 HSPs Collected Number of families returned by RECON: 973 Round Time: 00:05:35 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 67323 repeats masked totaling 15627002 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30020026 bp Num Contigs Represented = 133 Non ambiguous bp: Initial: 30013026 bp After Masking: 11899762 bp Masked: 60.35 % -- Input Database Coverage: 40026374 bp out of 3476679425 bp ( 1.15 % ) Sampling Time: 00:06:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 296835 Comparison Time: 00:10:16 (hh:mm:ss) Elapsed Time, 47799 HSPs Collected Number of families returned by RECON: 2963 Round Time: 00:17:44 (hh:mm:ss) Elapsed Time : 109 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 207395 repeats masked totaling 49054315 bp(s). - TE Masking time 00:00:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90027653 bp Num Contigs Represented = 355 Non ambiguous bp: Initial: 90008683 bp After Masking: 32824557 bp Masked: 63.53 % -- Input Database Coverage: 130054027 bp out of 3476679425 bp ( 3.74 % ) Sampling Time: 00:22:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2694681 Comparison Time: 00:51:12 (hh:mm:ss) Elapsed Time, 190879 HSPs Collected Number of families returned by RECON: 7622 Round Time: 01:16:18 (hh:mm:ss) Elapsed Time : 358 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:53:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 688382 repeats masked totaling 159491309 bp(s). - TE Masking time 00:03:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270076589 bp Num Contigs Represented = 790 Non ambiguous bp: Initial: 270021665 bp After Masking: 86832139 bp Masked: 67.84 % -- Input Database Coverage: 400130616 bp out of 3476679425 bp ( 11.51 % ) Sampling Time: 01:04:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23946660 Comparison Time: 04:40:20 (hh:mm:ss) Elapsed Time, 609544 HSPs Collected Number of families returned by RECON: 20650 Round Time: 05:55:29 (hh:mm:ss) Elapsed Time : 816 families discovered. RepeatScout/RECON discovery complete: 1805 families found Classification Time: 00:36:40 (hh:mm:ss) Elapsed Time Program Time: 08:24:12 (hh:mm:ss) Elapsed Time