RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.iuOpkY/RM_3804053.TueJan161026002024 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: 1705429557 Database = /dev/shm/rModeler.iuOpkY/GCF_030144855.1_sHypSab1.hap1 - Sequences = 2989 - Bases = 4044869043 - 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 |************************************************** [ 2956 ] Storage Throughput = good ( 771.09 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40021544 bp ( 40016544 non ambiguous ) - Num Contigs Represented = 159 - Sequence extraction : 00:02:42 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:56 (hh:mm:ss) Elapsed Time Round Time: 00:31:40 (hh:mm:ss) Elapsed Time : 658 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:37 (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... 18949 repeats masked totaling 4900033 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10037082 bp Num Contigs Represented = 77 Non ambiguous bp: Initial: 10035482 bp After Masking: 3294814 bp Masked: 67.17 % -- Input Database Coverage: 10037082 bp out of 4044869043 bp ( 0.25 % ) Sampling Time: 00:04:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33411 Comparison Time: 00:12:39 (hh:mm:ss) Elapsed Time, 3429 HSPs Collected Number of families returned by RECON: 631 Round Time: 00:17:24 (hh:mm:ss) Elapsed Time : 6 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 00:10:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 58143 repeats masked totaling 14977106 bp(s). - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30024485 bp Num Contigs Represented = 118 Non ambiguous bp: Initial: 30021085 bp After Masking: 10536405 bp Masked: 64.90 % -- Input Database Coverage: 40061567 bp out of 4044869043 bp ( 0.99 % ) Sampling Time: 00:13:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:38:41 (hh:mm:ss) Elapsed Time, 28971 HSPs Collected Number of families returned by RECON: 2029 Round Time: 00:53:59 (hh:mm:ss) Elapsed Time : 78 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:29:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 183173 repeats masked totaling 46859219 bp(s). - TE Masking time 00:01:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90016390 bp Num Contigs Represented = 332 Non ambiguous bp: Initial: 90006637 bp After Masking: 28945244 bp Masked: 67.84 % -- Input Database Coverage: 130077957 bp out of 4044869043 bp ( 3.22 % ) Sampling Time: 00:37:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2625486 Comparison Time: 02:28:29 (hh:mm:ss) Elapsed Time, 112992 HSPs Collected Number of families returned by RECON: 4587 Round Time: 03:10:30 (hh:mm:ss) Elapsed Time : 233 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:17:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:34:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 577696 repeats masked totaling 149195999 bp(s). - TE Masking time 00:07:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270022869 bp Num Contigs Represented = 738 Non ambiguous bp: Initial: 270001269 bp After Masking: 80201249 bp Masked: 70.30 % -- Input Database Coverage: 400100826 bp out of 4044869043 bp ( 9.89 % ) Sampling Time: 01:59:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23430435 Comparison Time: 11:31:00 (hh:mm:ss) Elapsed Time, 335562 HSPs Collected Number of families returned by RECON: 14740 Round Time: 13:42:31 (hh:mm:ss) Elapsed Time : 570 families discovered. RepeatScout/RECON discovery complete: 1545 families found Classification Time: 01:04:34 (hh:mm:ss) Elapsed Time Program Time: 19:40:38 (hh:mm:ss) Elapsed Time