RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.UwaODE/RM_3140292.WedJan101930532024 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: 1704943852 Database = /dev/shm/rModeler.UwaODE/GCF_011762505.1_mArvNil1.pat.X - Sequences = 1595 - Bases = 2496761438 - N50 = 86386494 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 155975538-167116563 | [ 1 ] 144834513-155975537 | [ 1 ] 133693489-144834513 | [ 2 ] 122552464-133693488 | [ 1 ] 111411440-122552464 | [ ] 100270415-111411439 | [ 2 ] 89129390-100270414 | [ 1 ] 77988366-89129390 | [ 6 ] 66847341-77988365 | [ 3 ] 55706317-66847341 | [ 1 ] 44565292-55706316 | [ 7 ] 33424267-44565291 | [ 2 ] 22283243-33424267 | [ 4 ] 11142218-22283242 | [ 1 ] 1194-11142218 |************************************************** [ 1563 ] Storage Throughput = excellent ( 1272.00 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40220046 bp ( 40019096 non ambiguous ) - Num Contigs Represented = 88 - Sequence extraction : 00:01:45 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:19 (hh:mm:ss) Elapsed Time Round Time: 00:25:50 (hh:mm:ss) Elapsed Time : 319 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:30 (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... 13081 repeats masked totaling 2365424 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10152554 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 10032183 bp After Masking: 7169531 bp Masked: 28.53 % -- Input Database Coverage: 10152554 bp out of 2496761438 bp ( 0.41 % ) Sampling Time: 00:02:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:06:32 (hh:mm:ss) Elapsed Time, 12785 HSPs Collected Number of families returned by RECON: 807 Round Time: 00:09:28 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 39866 repeats masked totaling 8081535 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30107488 bp Num Contigs Represented = 72 Non ambiguous bp: Initial: 30026909 bp After Masking: 20711830 bp Masked: 31.02 % -- Input Database Coverage: 40260042 bp out of 2496761438 bp ( 1.61 % ) Sampling Time: 00:05:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 290703 Comparison Time: 00:29:28 (hh:mm:ss) Elapsed Time, 21469 HSPs Collected Number of families returned by RECON: 2460 Round Time: 00:50:23 (hh:mm:ss) Elapsed Time : 52 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 129653 repeats masked totaling 25930282 bp(s). - TE Masking time 00:01:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90653990 bp Num Contigs Represented = 161 Non ambiguous bp: Initial: 90008102 bp After Masking: 60401989 bp Masked: 32.89 % -- Input Database Coverage: 130914032 bp out of 2496761438 bp ( 5.24 % ) Sampling Time: 00:16:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2641551 Comparison Time: 03:00:51 (hh:mm:ss) Elapsed Time, 109732 HSPs Collected Number of families returned by RECON: 9141 Round Time: 03:27:38 (hh:mm:ss) Elapsed Time : 183 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:37:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 428682 repeats masked totaling 86254709 bp(s). - TE Masking time 00:06:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272468906 bp Num Contigs Represented = 364 Non ambiguous bp: Initial: 270037269 bp After Masking: 172401894 bp Masked: 36.16 % -- Input Database Coverage: 403382938 bp out of 2496761438 bp ( 16.16 % ) Sampling Time: 00:57:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23905155 Comparison Time: 21:43:22 (hh:mm:ss) Elapsed Time, 285599 HSPs Collected Number of families returned by RECON: 36904 Round Time: 23:05:53 (hh:mm:ss) Elapsed Time : 424 families discovered. RepeatScout/RECON discovery complete: 993 families found Classification Time: 00:45:01 (hh:mm:ss) Elapsed Time Program Time: 28:44:13 (hh:mm:ss) Elapsed Time