RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.WnHs9M/RM_20398.TueDec51331192023 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: 1701811877 Database = /dev/shm/rModeler.WnHs9M/GCA_902686455.2_mSciVul1.2 - Sequences = 639 - Bases = 2878607543 - N50 = 162823747 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 198981385-213194295 | [ 2 ] 184768476-198981385 | [ 2 ] 170555567-184768476 | [ 2 ] 156342658-170555567 | [ 1 ] 142129749-156342658 | [ 3 ] 127916840-142129749 | [ 2 ] 113703931-127916840 | [ 1 ] 99491022-113703931 | [ 1 ] 85278113-99491022 | [ 2 ] 71065204-85278113 | [ 2 ] 56852295-71065204 | [ ] 42639386-56852295 | [ ] 28426477-42639386 | [ 2 ] 14213568-28426477 | [ 3 ] 659-14213568 |************************************************** [ 616 ] Storage Throughput = excellent ( 1137.56 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 42137364 bp ( 40013884 non ambiguous ) - Num Contigs Represented = 62 - Sequence extraction : 00:03:16 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:56 (hh:mm:ss) Elapsed Time Round Time: 00:34:38 (hh:mm:ss) Elapsed Time : 190 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9342 repeats masked totaling 2371790 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10621124 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 10011719 bp After Masking: 7577220 bp Masked: 24.32 % -- Input Database Coverage: 10621124 bp out of 2878607543 bp ( 0.37 % ) Sampling Time: 00:01:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 35511 Comparison Time: 00:07:12 (hh:mm:ss) Elapsed Time, 5830 HSPs Collected Number of families returned by RECON: 847 Round Time: 00:08:53 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30084 repeats masked totaling 7963747 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 31516160 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 30002085 bp After Masking: 21756401 bp Masked: 27.48 % -- Input Database Coverage: 42137284 bp out of 2878607543 bp ( 1.46 % ) Sampling Time: 00:04:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 312445 Comparison Time: 00:33:00 (hh:mm:ss) Elapsed Time, 23305 HSPs Collected Number of families returned by RECON: 2399 Round Time: 00:38:28 (hh:mm:ss) Elapsed Time : 54 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 101470 repeats masked totaling 26244917 bp(s). - TE Masking time 00:01:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 95536021 bp Num Contigs Represented = 94 Non ambiguous bp: Initial: 90035836 bp After Masking: 63021245 bp Masked: 30.00 % -- Input Database Coverage: 137673305 bp out of 2878607543 bp ( 4.78 % ) Sampling Time: 00:12:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2876401 Comparison Time: 03:58:58 (hh:mm:ss) Elapsed Time, 124094 HSPs Collected Number of families returned by RECON: 8260 Round Time: 04:19:01 (hh:mm:ss) Elapsed Time : 179 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:21:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 347354 repeats masked totaling 88703283 bp(s). - TE Masking time 00:06:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 285351734 bp Num Contigs Represented = 155 Non ambiguous bp: Initial: 270004980 bp After Masking: 179178756 bp Masked: 33.64 % -- Input Database Coverage: 423025039 bp out of 2878607543 bp ( 14.70 % ) Sampling Time: 00:38:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 25665030 Comparison Time: 30:17:51 (hh:mm:ss) Elapsed Time, 442938 HSPs Collected Number of families returned by RECON: 36508 Round Time: 31:34:54 (hh:mm:ss) Elapsed Time : 377 families discovered. RepeatScout/RECON discovery complete: 820 families found Classification Time: 00:51:41 (hh:mm:ss) Elapsed Time Program Time: 38:07:35 (hh:mm:ss) Elapsed Time