RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.yMrm5b/RM_5969.MonJul150546442024 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: 1721047603 Database = /dev/shm/rModeler.yMrm5b/GCF_008315115.2_SLUC_FBN_1.2 - Sequences = 337 - Bases = 901238333 - N50 = 42110657 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 50767453-54393628 | [ 1 ] 47141278-50767452 | [ 1 ] 43515103-47141277 | [ 4 ] 39888929-43515103 | [ 5 ] 36262754-39888928 | [ 2 ] 32636579-36262753 | [ 2 ] 29010404-32636578 |* [ 7 ] 25384230-29010404 | [ ] 21758055-25384229 | [ ] 18131880-21758054 | [ 2 ] 14505705-18131879 | [ ] 10879531-14505705 | [ ] 7253356-10879530 | [ ] 3627181-7253355 | [ ] 1007-3627181 |************************************************** [ 313 ] Storage Throughput = good ( 994.70 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40006791 bp ( 40002449 non ambiguous ) - Num Contigs Represented = 45 - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:23:13 (hh:mm:ss) Elapsed Time Round Time: 00:35:26 (hh:mm:ss) Elapsed Time : 1104 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14475 repeats masked totaling 2513208 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10015953 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10013749 bp After Masking: 6979464 bp Masked: 30.30 % -- Input Database Coverage: 10015953 bp out of 901238333 bp ( 1.11 % ) Sampling Time: 00:03:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:06:12 (hh:mm:ss) Elapsed Time, 11488 HSPs Collected Number of families returned by RECON: 1670 Round Time: 00:09:52 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44574 repeats masked totaling 8176626 bp(s). - TE Masking time 00:00:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30030909 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 30028771 bp After Masking: 19935935 bp Masked: 33.61 % -- Input Database Coverage: 40046862 bp out of 901238333 bp ( 4.44 % ) Sampling Time: 00:07:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:30:13 (hh:mm:ss) Elapsed Time, 50738 HSPs Collected Number of families returned by RECON: 5470 Round Time: 00:40:14 (hh:mm:ss) Elapsed Time : 116 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 142430 repeats masked totaling 24719265 bp(s). - TE Masking time 00:03:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90059417 bp Num Contigs Represented = 59 Non ambiguous bp: Initial: 90034558 bp After Masking: 59567892 bp Masked: 33.84 % -- Input Database Coverage: 130106279 bp out of 901238333 bp ( 14.44 % ) Sampling Time: 00:23:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2588950 Comparison Time: 03:21:49 (hh:mm:ss) Elapsed Time, 352818 HSPs Collected Number of families returned by RECON: 16852 Round Time: 04:04:01 (hh:mm:ss) Elapsed Time : 736 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:55:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 499971 repeats masked totaling 89904322 bp(s). - TE Masking time 00:16:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270099043 bp Num Contigs Represented = 125 Non ambiguous bp: Initial: 270015898 bp After Masking: 163024174 bp Masked: 39.62 % -- Input Database Coverage: 400205322 bp out of 901238333 bp ( 44.41 % ) Sampling Time: 01:18:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23314206 Comparison Time: 32:06:34 (hh:mm:ss) Elapsed Time, 980718 HSPs Collected Number of families returned by RECON: 52846 Round Time: 35:47:43 (hh:mm:ss) Elapsed Time : 1632 families discovered. RepeatScout/RECON discovery complete: 3598 families found Classification Time: 02:21:45 (hh:mm:ss) Elapsed Time Program Time: 43:39:01 (hh:mm:ss) Elapsed Time