RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.8NmZdK/RM_725127.FriDec61846492024 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: 1733539608 Database = /scratch/tmp/rModeler.8NmZdK/GCA_964194165.1_sCetMax3.hap2.1 - Sequences = 3829 - Bases = 3817333378 - N50 = 143366049 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 229645941-246049152 | [ 1 ] 213242731-229645941 | [ 1 ] 196839521-213242731 | [ 1 ] 180436311-196839521 | [ ] 164033101-180436311 | [ 2 ] 147629891-164033101 | [ 2 ] 131226681-147629891 | [ 3 ] 114823470-131226680 | [ 4 ] 98420260-114823470 | [ 5 ] 82017050-98420260 | [ 2 ] 65613840-82017050 | [ 1 ] 49210630-65613840 | [ 2 ] 32807420-49210630 | [ 2 ] 16404210-32807420 | [ 7 ] 1000-16404210 |************************************************** [ 3796 ] Storage Throughput = excellent ( 1471.56 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40007249 bp ( 40002849 non ambiguous ) - Num Contigs Represented = 144 - Sequence extraction : 00:01:19 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:18 (hh:mm:ss) Elapsed Time Round Time: 00:12:10 (hh:mm:ss) Elapsed Time : 548 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16883 repeats masked totaling 5205263 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027445 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 10026445 bp After Masking: 3942166 bp Masked: 60.68 % -- Input Database Coverage: 10027445 bp out of 3817333378 bp ( 0.26 % ) Sampling Time: 00:02:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:02:37 (hh:mm:ss) Elapsed Time, 6011 HSPs Collected Number of families returned by RECON: 939 Round Time: 00:05:04 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 50721 repeats masked totaling 16229829 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30019725 bp Num Contigs Represented = 115 Non ambiguous bp: Initial: 30016325 bp After Masking: 11115702 bp Masked: 62.97 % -- Input Database Coverage: 40047170 bp out of 3817333378 bp ( 1.05 % ) Sampling Time: 00:07:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 296065 Comparison Time: 00:09:05 (hh:mm:ss) Elapsed Time, 41627 HSPs Collected Number of families returned by RECON: 2745 Round Time: 00:16:49 (hh:mm:ss) Elapsed Time : 103 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 161009 repeats masked totaling 51476662 bp(s). - TE Masking time 00:00:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90026381 bp Num Contigs Represented = 259 Non ambiguous bp: Initial: 90011282 bp After Masking: 30082988 bp Masked: 66.58 % -- Input Database Coverage: 130073551 bp out of 3817333378 bp ( 3.41 % ) Sampling Time: 00:21:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2625486 Comparison Time: 00:41:42 (hh:mm:ss) Elapsed Time, 152237 HSPs Collected Number of families returned by RECON: 6972 Round Time: 01:07:17 (hh:mm:ss) Elapsed Time : 310 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:48:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 531073 repeats masked totaling 165136344 bp(s). - TE Masking time 00:03:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270062802 bp Num Contigs Represented = 595 Non ambiguous bp: Initial: 270024902 bp After Masking: 81107423 bp Masked: 69.96 % -- Input Database Coverage: 400136353 bp out of 3817333378 bp ( 10.48 % ) Sampling Time: 01:01:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23670640 Comparison Time: 04:03:00 (hh:mm:ss) Elapsed Time, 382225 HSPs Collected Number of families returned by RECON: 19747 Round Time: 05:12:26 (hh:mm:ss) Elapsed Time : 693 families discovered. RepeatScout/RECON discovery complete: 1666 families found Classification Time: 00:31:35 (hh:mm:ss) Elapsed Time Program Time: 07:25:21 (hh:mm:ss) Elapsed Time