RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.rGQXvZ/RM_28726.WedJul240747132024 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: 1721832425 Database = /dev/shm/rModeler.rGQXvZ/GCF_019176455.1_IFAPA_SoseM_1 - Sequences = 1937 - Bases = 603535267 - N50 = 26846769 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 40062433-42924012 | [ 1 ] 37200854-40062432 | [ ] 34339275-37200853 | [ 1 ] 31477696-34339274 | [ 1 ] 28616117-31477695 | [ ] 25754538-28616116 | [ 8 ] 22892959-25754537 | [ 4 ] 20031381-22892959 | [ 4 ] 17169802-20031380 | [ 2 ] 14308223-17169801 | [ ] 11446644-14308222 | [ ] 8585065-11446643 | [ ] 5723486-8585064 | [ ] 2861907-5723485 | [ ] 329-2861907 |************************************************** [ 1916 ] Storage Throughput = good ( 753.03 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40016819 bp ( 40011619 non ambiguous ) - Num Contigs Represented = 191 - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:41 (hh:mm:ss) Elapsed Time Round Time: 00:35:34 (hh:mm:ss) Elapsed Time : 466 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9666 repeats masked totaling 1099395 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10006872 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 10005872 bp After Masking: 8589342 bp Masked: 14.16 % -- Input Database Coverage: 10006872 bp out of 603535267 bp ( 1.66 % ) Sampling Time: 00:01:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 36856 Comparison Time: 00:49:40 (hh:mm:ss) Elapsed Time, 9520 HSPs Collected Number of families returned by RECON: 1900 Round Time: 00:52:49 (hh:mm:ss) Elapsed Time : 23 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32842 repeats masked totaling 3669624 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30009944 bp Num Contigs Represented = 147 Non ambiguous bp: Initial: 30005744 bp After Masking: 25386607 bp Masked: 15.39 % -- Input Database Coverage: 40016816 bp out of 603535267 bp ( 6.63 % ) Sampling Time: 00:02:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 322003 Comparison Time: 02:48:07 (hh:mm:ss) Elapsed Time, 70992 HSPs Collected Number of families returned by RECON: 7335 Round Time: 02:59:35 (hh:mm:ss) Elapsed Time : 150 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 115642 repeats masked totaling 13250874 bp(s). - TE Masking time 00:01:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90028608 bp Num Contigs Represented = 351 Non ambiguous bp: Initial: 90017898 bp After Masking: 74001921 bp Masked: 17.79 % -- Input Database Coverage: 130045424 bp out of 603535267 bp ( 21.55 % ) Sampling Time: 00:08:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2922153 Comparison Time: 11:13:45 (hh:mm:ss) Elapsed Time, 328679 HSPs Collected Number of families returned by RECON: 25851 Round Time: 12:01:44 (hh:mm:ss) Elapsed Time : 477 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 425025 repeats masked totaling 52511651 bp(s). - TE Masking time 00:10:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270053055 bp Num Contigs Represented = 987 Non ambiguous bp: Initial: 270025447 bp After Masking: 208979801 bp Masked: 22.61 % -- Input Database Coverage: 400098479 bp out of 603535267 bp ( 66.29 % ) Sampling Time: 00:29:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 26626753 Comparison Time: 55:43:50 (hh:mm:ss) Elapsed Time, 1050575 HSPs Collected Number of families returned by RECON: 90819 Round Time: 59:47:30 (hh:mm:ss) Elapsed Time : 1084 families discovered. RepeatScout/RECON discovery complete: 2200 families found Classification Time: 01:33:57 (hh:mm:ss) Elapsed Time Program Time: 77:51:09 (hh:mm:ss) Elapsed Time