RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.wsjMtJ/RM_31020.MonJan20327182023 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: 1672658837 Database = /dev/shm/rModeler.wsjMtJ/GCF_015220745.1_fSebUmb1.pri - Sequences = 138 - Bases = 800904020 - N50 = 34964250 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 41126569-44063945 |* [ 3 ] 38189194-41126569 | [ 2 ] 35251818-38189193 |* [ 3 ] 32314443-35251818 |*** [ 7 ] 29377068-32314443 |* [ 3 ] 26439692-29377067 |* [ 3 ] 23502317-26439692 | [ 1 ] 20564941-23502316 | [ 1 ] 17627566-20564941 | [ ] 14690191-17627566 | [ 1 ] 11752815-14690190 | [ ] 8815440-11752815 | [ ] 5878064-8815439 | [ ] 2940689-5878064 | [ ] 3314-2940689 |************************************************** [ 114 ] Storage Throughput = good ( 763.64 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40212418 bp ( 40019802 non ambiguous ) - Num Contigs Represented = 39 - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:50 (hh:mm:ss) Elapsed Time Round Time: 00:25:23 (hh:mm:ss) Elapsed Time : 917 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 00:00:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17351 repeats masked totaling 2664753 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10072637 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10032637 bp After Masking: 6918020 bp Masked: 31.04 % -- Input Database Coverage: 10072637 bp out of 800904020 bp ( 1.26 % ) Sampling Time: 00:01:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:06:01 (hh:mm:ss) Elapsed Time, 8585 HSPs Collected Number of families returned by RECON: 1349 Round Time: 00:08:20 (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 : 00:00:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 51724 repeats masked totaling 7914623 bp(s). - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30179781 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 30027165 bp After Masking: 20536887 bp Masked: 31.61 % -- Input Database Coverage: 40252418 bp out of 800904020 bp ( 5.03 % ) Sampling Time: 00:05:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:30:23 (hh:mm:ss) Elapsed Time, 47130 HSPs Collected Number of families returned by RECON: 4989 Round Time: 00:37:33 (hh:mm:ss) Elapsed Time : 128 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 163679 repeats masked totaling 24778617 bp(s). - TE Masking time 00:02:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90080575 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 90010014 bp After Masking: 61176308 bp Masked: 32.03 % -- Input Database Coverage: 130332993 bp out of 800904020 bp ( 16.27 % ) Sampling Time: 00:12:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 03:27:59 (hh:mm:ss) Elapsed Time, 277614 HSPs Collected Number of families returned by RECON: 17094 Round Time: 03:56:03 (hh:mm:ss) Elapsed Time : 598 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 569154 repeats masked totaling 87102853 bp(s). - TE Masking time 00:12:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270352772 bp Num Contigs Represented = 84 Non ambiguous bp: Initial: 270024239 bp After Masking: 170868626 bp Masked: 36.72 % -- Input Database Coverage: 400685765 bp out of 800904020 bp ( 50.03 % ) Sampling Time: 00:43:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22980810 Comparison Time: 25:45:25 (hh:mm:ss) Elapsed Time, 796342 HSPs Collected Number of families returned by RECON: 59485 Round Time: 28:27:39 (hh:mm:ss) Elapsed Time : 1341 families discovered. RepeatScout/RECON discovery complete: 2996 families found Classification Time: 01:34:56 (hh:mm:ss) Elapsed Time Program Time: 35:09:54 (hh:mm:ss) Elapsed Time