RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.s7DEeN/RM_2281584.MonNov182234032024 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: 1731998042 Database = /scratch/tmp/rModeler.s7DEeN/GCA_964165515.1_mMesBid2.hap1.1 - Sequences = 1602 - Bases = 2999098505 - N50 = 114121756 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 214747525-230086563 | [ 1 ] 199408487-214747524 | [ ] 184069450-199408487 | [ 1 ] 168730412-184069449 | [ 2 ] 153391375-168730412 | [ ] 138052337-153391374 | [ 2 ] 122713300-138052337 | [ ] 107374262-122713299 | [ 3 ] 92035225-107374262 | [ 4 ] 76696187-92035224 | [ 5 ] 61357150-76696187 | [ 1 ] 46018112-61357149 | [ 2 ] 30679075-46018112 | [ 1 ] 15340037-30679074 | [ ] 1000-15340037 |************************************************** [ 1580 ] Storage Throughput = excellent ( 1487.97 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40002816 bp ( 40000016 non ambiguous ) - Num Contigs Represented = 172 - Sequence extraction : 00:01:06 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:58 (hh:mm:ss) Elapsed Time Round Time: 00:16:29 (hh:mm:ss) Elapsed Time : 211 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 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10518 repeats masked totaling 3060419 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10006873 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 10005673 bp After Masking: 6382619 bp Masked: 36.21 % -- Input Database Coverage: 10006873 bp out of 2999098505 bp ( 0.33 % ) Sampling Time: 00:00:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:02:59 (hh:mm:ss) Elapsed Time, 71074 HSPs Collected Number of families returned by RECON: 531 Round Time: 00:04:18 (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 : 00:00:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 35218 repeats masked totaling 10862399 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30035785 bp Num Contigs Represented = 139 Non ambiguous bp: Initial: 30034185 bp After Masking: 17741616 bp Masked: 40.93 % -- Input Database Coverage: 40042658 bp out of 2999098505 bp ( 1.34 % ) Sampling Time: 00:01:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:11:46 (hh:mm:ss) Elapsed Time, 33334 HSPs Collected Number of families returned by RECON: 2300 Round Time: 00:14:14 (hh:mm:ss) Elapsed Time : 53 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 113023 repeats masked totaling 34271049 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90031443 bp Num Contigs Represented = 311 Non ambiguous bp: Initial: 90025843 bp After Masking: 51022381 bp Masked: 43.32 % -- Input Database Coverage: 130074101 bp out of 2999098505 bp ( 4.34 % ) Sampling Time: 00:06:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2582128 Comparison Time: 01:04:14 (hh:mm:ss) Elapsed Time, 189386 HSPs Collected Number of families returned by RECON: 7389 Round Time: 01:12:16 (hh:mm:ss) Elapsed Time : 166 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 374267 repeats masked totaling 110809099 bp(s). - TE Masking time 00:02:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270056149 bp Num Contigs Represented = 655 Non ambiguous bp: Initial: 270035472 bp After Masking: 145981394 bp Masked: 45.94 % -- Input Database Coverage: 400130250 bp out of 2999098505 bp ( 13.34 % ) Sampling Time: 00:17:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23266431 Comparison Time: 07:05:42 (hh:mm:ss) Elapsed Time, 1544736 HSPs Collected Number of families returned by RECON: 27775 Round Time: 07:35:35 (hh:mm:ss) Elapsed Time : 387 families discovered. RepeatScout/RECON discovery complete: 832 families found Classification Time: 00:25:44 (hh:mm:ss) Elapsed Time Program Time: 09:48:36 (hh:mm:ss) Elapsed Time