RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.0yR8fv/RM_4953.SatDec20931172023 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: 1701538276 Database = /dev/shm/rModeler.0yR8fv/GCA_030144855.1_sHypSab1.hap1 - Sequences = 2990 - Bases = 4044886845 - N50 = 167937546 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 200495607-214816651 | [ 2 ] 186174564-200495607 | [ 3 ] 171853520-186174563 | [ 3 ] 157532477-171853520 | [ 2 ] 143211434-157532477 | [ ] 128890390-143211433 | [ ] 114569347-128890390 | [ 1 ] 100248303-114569346 | [ 3 ] 85927260-100248303 | [ 3 ] 71606217-85927260 | [ 3 ] 57285173-71606216 | [ 4 ] 42964130-57285173 | [ 5 ] 28643086-42964129 | [ 4 ] 14322043-28643086 | [ ] 1000-14322043 |************************************************** [ 2957 ] Storage Throughput = excellent ( 1193.47 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40030892 bp ( 40026092 non ambiguous ) - Num Contigs Represented = 170 - Sequence extraction : 00:02:32 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:39 (hh:mm:ss) Elapsed Time Round Time: 00:34:19 (hh:mm:ss) Elapsed Time : 626 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18158 repeats masked totaling 4825274 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10029992 bp Num Contigs Represented = 64 Non ambiguous bp: Initial: 10029192 bp After Masking: 3533965 bp Masked: 64.76 % -- Input Database Coverage: 10029992 bp out of 4044886845 bp ( 0.25 % ) Sampling Time: 00:04:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:04:26 (hh:mm:ss) Elapsed Time, 3390 HSPs Collected Number of families returned by RECON: 590 Round Time: 00:08:56 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 57386 repeats masked totaling 15126220 bp(s). - TE Masking time 00:00:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30040900 bp Num Contigs Represented = 142 Non ambiguous bp: Initial: 30036900 bp After Masking: 10486569 bp Masked: 65.09 % -- Input Database Coverage: 40070892 bp out of 4044886845 bp ( 0.99 % ) Sampling Time: 00:14:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 292230 Comparison Time: 00:18:57 (hh:mm:ss) Elapsed Time, 25073 HSPs Collected Number of families returned by RECON: 1799 Round Time: 00:34:58 (hh:mm:ss) Elapsed Time : 67 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:31:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 177591 repeats masked totaling 46658938 bp(s). - TE Masking time 00:02:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90044009 bp Num Contigs Represented = 326 Non ambiguous bp: Initial: 90036278 bp After Masking: 29817445 bp Masked: 66.88 % -- Input Database Coverage: 130114901 bp out of 4044886845 bp ( 3.22 % ) Sampling Time: 00:39:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2607186 Comparison Time: 01:45:13 (hh:mm:ss) Elapsed Time, 127824 HSPs Collected Number of families returned by RECON: 4907 Round Time: 02:30:04 (hh:mm:ss) Elapsed Time : 274 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:17:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:41:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 566928 repeats masked totaling 150001879 bp(s). - TE Masking time 00:09:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270052111 bp Num Contigs Represented = 761 Non ambiguous bp: Initial: 270027911 bp After Masking: 78773348 bp Masked: 70.83 % -- Input Database Coverage: 400167012 bp out of 4044886845 bp ( 9.89 % ) Sampling Time: 02:08:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23492085 Comparison Time: 11:37:50 (hh:mm:ss) Elapsed Time, 276836 HSPs Collected Number of families returned by RECON: 14188 Round Time: 14:00:08 (hh:mm:ss) Elapsed Time : 516 families discovered. RepeatScout/RECON discovery complete: 1490 families found Classification Time: 01:10:36 (hh:mm:ss) Elapsed Time Program Time: 18:59:02 (hh:mm:ss) Elapsed Time