RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ItcJCy/RM_29349.WedJan101934192024 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: 1704944059 Database = /dev/shm/rModeler.ItcJCy/GCA_015852565.1_bf_hap-2 - Sequences = 341 - Bases = 490782628 - N50 = 25385209 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 32126994-34421708 | [ 4 ] 29832280-32126993 | [ ] 27537566-29832279 | [ ] 25242852-27537565 | [ 4 ] 22948138-25242851 | [ 4 ] 20653424-22948137 | [ 4 ] 18358710-20653423 | [ 2 ] 16063997-18358710 | [ 1 ] 13769283-16063996 | [ ] 11474569-13769282 | [ ] 9179855-11474568 | [ ] 6885141-9179854 | [ ] 4590427-6885140 | [ ] 2295713-4590426 | [ ] 1000-2295713 |************************************************** [ 322 ] Storage Throughput = excellent ( 1064.81 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40026702 bp ( 40016759 non ambiguous ) - Num Contigs Represented = 48 - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:51 (hh:mm:ss) Elapsed Time Round Time: 00:24:23 (hh:mm:ss) Elapsed Time : 743 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13913 repeats masked totaling 2359420 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10005358 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10004358 bp After Masking: 7038056 bp Masked: 29.65 % -- Input Database Coverage: 10005358 bp out of 490782628 bp ( 2.04 % ) Sampling Time: 00:01:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:05:01 (hh:mm:ss) Elapsed Time, 6323 HSPs Collected Number of families returned by RECON: 1168 Round Time: 00:06:22 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43451 repeats masked totaling 7436520 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30021330 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 30012387 bp After Masking: 20345663 bp Masked: 32.21 % -- Input Database Coverage: 40026688 bp out of 490782628 bp ( 8.16 % ) Sampling Time: 00:03:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 290703 Comparison Time: 00:25:09 (hh:mm:ss) Elapsed Time, 35620 HSPs Collected Number of families returned by RECON: 4251 Round Time: 00:30:14 (hh:mm:ss) Elapsed Time : 71 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 135694 repeats masked totaling 22759351 bp(s). - TE Masking time 00:02:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90036743 bp Num Contigs Represented = 99 Non ambiguous bp: Initial: 90022743 bp After Masking: 61241459 bp Masked: 31.97 % -- Input Database Coverage: 130063431 bp out of 490782628 bp ( 26.50 % ) Sampling Time: 00:09:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2616328 Comparison Time: 02:54:47 (hh:mm:ss) Elapsed Time, 256065 HSPs Collected Number of families returned by RECON: 14907 Round Time: 03:17:38 (hh:mm:ss) Elapsed Time : 480 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 464310 repeats masked totaling 80469460 bp(s). - TE Masking time 00:11:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270085364 bp Num Contigs Represented = 210 Non ambiguous bp: Initial: 270039307 bp After Masking: 172121913 bp Masked: 36.26 % -- Input Database Coverage: 400148795 bp out of 490782628 bp ( 81.53 % ) Sampling Time: 00:34:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23457825 Comparison Time: 22:19:59 (hh:mm:ss) Elapsed Time, 966818 HSPs Collected Number of families returned by RECON: 51573 Round Time: 24:41:08 (hh:mm:ss) Elapsed Time : 1259 families discovered. RepeatScout/RECON discovery complete: 2566 families found Classification Time: 02:08:17 (hh:mm:ss) Elapsed Time Program Time: 31:08:02 (hh:mm:ss) Elapsed Time