RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.FWmRtZ/RM_3536658.MonJun241444352024 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: 1719265475 Database = /dev/shm/rModeler.FWmRtZ/GCF_963924245.1_bChrRid1.1 - Sequences = 728 - Bases = 1417554307 - N50 = 95717064 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 206184293-220911672 | [ 1 ] 191456915-206184293 | [ ] 176729537-191456915 | [ ] 162002159-176729537 | [ 1 ] 147274781-162002159 | [ ] 132547403-147274781 | [ ] 117820025-132547403 | [ 1 ] 103092646-117820024 | [ ] 88365268-103092646 | [ 1 ] 73637890-88365268 | [ 3 ] 58910512-73637890 | [ 1 ] 44183134-58910512 | [ 2 ] 29455756-44183134 | [ ] 14728378-29455756 | [ 5 ] 1000-14728378 |************************************************** [ 713 ] Storage Throughput = excellent ( 1309.67 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40031567 bp ( 40027767 non ambiguous ) - Num Contigs Represented = 135 - Sequence extraction : 00:01:50 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:57 (hh:mm:ss) Elapsed Time Round Time: 00:32:28 (hh:mm:ss) Elapsed Time : 60 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2558 repeats masked totaling 931805 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10018050 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 10017050 bp After Masking: 8077194 bp Masked: 19.37 % -- Input Database Coverage: 10018050 bp out of 1417554307 bp ( 0.71 % ) Sampling Time: 00:01:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:40 (hh:mm:ss) Elapsed Time, 2759 HSPs Collected Number of families returned by RECON: 178 Round Time: 00:07:03 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9530 repeats masked totaling 3428144 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30013437 bp Num Contigs Represented = 118 Non ambiguous bp: Initial: 30010637 bp After Masking: 23742935 bp Masked: 20.88 % -- Input Database Coverage: 40031487 bp out of 1417554307 bp ( 2.82 % ) Sampling Time: 00:04:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:28:38 (hh:mm:ss) Elapsed Time, 19359 HSPs Collected Number of families returned by RECON: 1117 Round Time: 00:33:27 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 25700 repeats masked totaling 9264334 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90020425 bp Num Contigs Represented = 207 Non ambiguous bp: Initial: 90013825 bp After Masking: 72413684 bp Masked: 19.55 % -- Input Database Coverage: 130051912 bp out of 1417554307 bp ( 9.17 % ) Sampling Time: 00:09:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2584401 Comparison Time: 03:17:38 (hh:mm:ss) Elapsed Time, 30537 HSPs Collected Number of families returned by RECON: 6525 Round Time: 03:29:51 (hh:mm:ss) Elapsed Time : 56 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 88645 repeats masked totaling 31099600 bp(s). - TE Masking time 00:02:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270041999 bp Num Contigs Represented = 408 Non ambiguous bp: Initial: 270027399 bp After Masking: 213082888 bp Masked: 21.09 % -- Input Database Coverage: 400093911 bp out of 1417554307 bp ( 28.22 % ) Sampling Time: 00:33:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23280076 Comparison Time: 25:52:25 (hh:mm:ss) Elapsed Time, 167049 HSPs Collected Number of families returned by RECON: 40937 Round Time: 26:48:24 (hh:mm:ss) Elapsed Time : 216 families discovered. RepeatScout/RECON discovery complete: 341 families found Classification Time: 00:33:08 (hh:mm:ss) Elapsed Time Program Time: 32:04:21 (hh:mm:ss) Elapsed Time