RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.FKgHQ2/RM_30551.SunDec30251502023 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: 1701600708 Database = /dev/shm/rModeler.FKgHQ2/GCA_030448965.1_fSalBra1.hap1 - Sequences = 182 - Bases = 1078246036 - N50 = 42738157 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 95143863-101938685 | [ 1 ] 88349041-95143862 | [ ] 81554220-88349041 | [ ] 74759398-81554219 | [ ] 67964576-74759397 | [ ] 61169755-67964576 | [ ] 54374933-61169754 | [ 1 ] 47580111-54374932 | [ 2 ] 40785290-47580111 |* [ 6 ] 33990468-40785289 |*** [ 10 ] 27195646-33990467 |* [ 4 ] 20400825-27195646 | [ ] 13606003-20400824 | [ 1 ] 6811181-13606002 | [ 1 ] 16360-6811181 |************************************************** [ 156 ] Storage Throughput = excellent ( 1154.80 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40655162 bp ( 40000492 non ambiguous ) - Num Contigs Represented = 46 - Sequence extraction : 00:00:59 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:51 (hh:mm:ss) Elapsed Time Round Time: 00:36:49 (hh:mm:ss) Elapsed Time : 769 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16539 repeats masked totaling 2453088 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10245040 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 10001003 bp After Masking: 6499975 bp Masked: 35.01 % -- Input Database Coverage: 10245040 bp out of 1078246036 bp ( 0.95 % ) Sampling Time: 00:01:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:05:34 (hh:mm:ss) Elapsed Time, 8301 HSPs Collected Number of families returned by RECON: 1471 Round Time: 00:07:49 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 50563 repeats masked totaling 7612433 bp(s). - TE Masking time 00:00:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30450042 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 30039409 bp After Masking: 18681583 bp Masked: 37.81 % -- Input Database Coverage: 40695082 bp out of 1078246036 bp ( 3.77 % ) Sampling Time: 00:06:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 292230 Comparison Time: 00:27:37 (hh:mm:ss) Elapsed Time, 72133 HSPs Collected Number of families returned by RECON: 5597 Round Time: 00:36:32 (hh:mm:ss) Elapsed Time : 173 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 168392 repeats masked totaling 23821237 bp(s). - TE Masking time 00:02:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91481016 bp Num Contigs Represented = 78 Non ambiguous bp: Initial: 90035342 bp After Masking: 55637664 bp Masked: 38.20 % -- Input Database Coverage: 132176098 bp out of 1078246036 bp ( 12.26 % ) Sampling Time: 00:16:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2625486 Comparison Time: 03:16:56 (hh:mm:ss) Elapsed Time, 296064 HSPs Collected Number of families returned by RECON: 17342 Round Time: 04:20:32 (hh:mm:ss) Elapsed Time : 470 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:36:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 601703 repeats masked totaling 86579111 bp(s). - TE Masking time 00:13:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 275915070 bp Num Contigs Represented = 114 Non ambiguous bp: Initial: 270013657 bp After Masking: 152093181 bp Masked: 43.67 % -- Input Database Coverage: 408091168 bp out of 1078246036 bp ( 37.85 % ) Sampling Time: 00:57:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24029778 Comparison Time: 23:29:59 (hh:mm:ss) Elapsed Time, 899888 HSPs Collected Number of families returned by RECON: 53743 Round Time: 26:15:32 (hh:mm:ss) Elapsed Time : 1089 families discovered. RepeatScout/RECON discovery complete: 2515 families found Classification Time: 01:46:15 (hh:mm:ss) Elapsed Time Program Time: 33:43:29 (hh:mm:ss) Elapsed Time