RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.syIbFS/RM_1180255.TueNov121203092024 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: 1731441788 Database = /scratch/tmp/rModeler.syIbFS/GCA_964194155.1_sCetMax3.hap1.1 - Sequences = 5088 - Bases = 3993866540 - N50 = 129010711 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 233511251-250190555 | [ 1 ] 216831947-233511250 | [ 1 ] 200152644-216831947 | [ 1 ] 183473340-200152643 | [ ] 166794036-183473339 | [ 2 ] 150114733-166794036 | [ 1 ] 133435429-150114732 | [ 4 ] 116756125-133435428 | [ 3 ] 100076822-116756125 | [ 5 ] 83397518-100076821 | [ 3 ] 66718214-83397517 | [ 1 ] 50038911-66718214 | [ 2 ] 33359607-50038910 | [ 2 ] 16680303-33359606 | [ 7 ] 1000-16680303 |************************************************** [ 5055 ] Storage Throughput = excellent ( 1598.91 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40012327 bp ( 40006327 non ambiguous ) - Num Contigs Represented = 172 - Sequence extraction : 00:01:12 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:15 (hh:mm:ss) Elapsed Time Round Time: 00:13:19 (hh:mm:ss) Elapsed Time : 560 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17227 repeats masked totaling 5241873 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10034432 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 10032632 bp After Masking: 3865411 bp Masked: 61.47 % -- Input Database Coverage: 10034432 bp out of 3993866540 bp ( 0.25 % ) Sampling Time: 00:02:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:02:31 (hh:mm:ss) Elapsed Time, 6583 HSPs Collected Number of families returned by RECON: 955 Round Time: 00:05:15 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 50729 repeats masked totaling 15445080 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30017815 bp Num Contigs Represented = 152 Non ambiguous bp: Initial: 30013615 bp After Masking: 10552193 bp Masked: 64.84 % -- Input Database Coverage: 40052247 bp out of 3993866540 bp ( 1.00 % ) Sampling Time: 00:10:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 292995 Comparison Time: 00:09:42 (hh:mm:ss) Elapsed Time, 39587 HSPs Collected Number of families returned by RECON: 2578 Round Time: 00:21:13 (hh:mm:ss) Elapsed Time : 87 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:26:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 157779 repeats masked totaling 49561625 bp(s). - TE Masking time 00:00:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90042040 bp Num Contigs Represented = 337 Non ambiguous bp: Initial: 90026440 bp After Masking: 29628888 bp Masked: 67.09 % -- Input Database Coverage: 130094287 bp out of 3993866540 bp ( 3.26 % ) Sampling Time: 00:29:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2655360 Comparison Time: 00:50:08 (hh:mm:ss) Elapsed Time, 161529 HSPs Collected Number of families returned by RECON: 7078 Round Time: 01:24:09 (hh:mm:ss) Elapsed Time : 295 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:04:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 520621 repeats masked totaling 158720768 bp(s). - TE Masking time 00:03:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270052066 bp Num Contigs Represented = 830 Non ambiguous bp: Initial: 270011760 bp After Masking: 80268167 bp Masked: 70.27 % -- Input Database Coverage: 400146353 bp out of 3993866540 bp ( 10.02 % ) Sampling Time: 01:16:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24085270 Comparison Time: 04:50:42 (hh:mm:ss) Elapsed Time, 616961 HSPs Collected Number of families returned by RECON: 19701 Round Time: 06:16:52 (hh:mm:ss) Elapsed Time : 693 families discovered. RepeatScout/RECON discovery complete: 1655 families found Classification Time: 00:32:54 (hh:mm:ss) Elapsed Time Program Time: 08:53:42 (hh:mm:ss) Elapsed Time