RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.jpggPH/RM_4126.ThuDec291741562022 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: 1672364514 Database = /dev/shm/rModeler.jpggPH/GCF_900324485.2_fMasArm1.2 - Sequences = 123 - Bases = 591951587 - N50 = 25822229 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 27182527-29124071 |*** [ 6 ] 25240984-27182527 |** [ 4 ] 23299441-25240984 |** [ 4 ] 21357898-23299441 |* [ 3 ] 19416355-21357898 |** [ 5 ] 17474812-19416355 | [ ] 15533269-17474812 | [ 1 ] 13591725-15533268 | [ ] 11650182-13591725 | [ ] 9708639-11650182 | [ 1 ] 7767096-9708639 | [ ] 5825553-7767096 | [ ] 3884010-5825553 | [ ] 1942467-3884010 |* [ 3 ] 924-1942467 |************************************************** [ 96 ] Storage Throughput = excellent ( 1216.54 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40980090 bp ( 40019309 non ambiguous ) - Num Contigs Represented = 40 - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:54 (hh:mm:ss) Elapsed Time Round Time: 00:24:34 (hh:mm:ss) Elapsed Time : 235 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3348 repeats masked totaling 1009937 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10204629 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10008098 bp After Masking: 8844250 bp Masked: 11.63 % -- Input Database Coverage: 10204629 bp out of 591951587 bp ( 1.72 % ) Sampling Time: 00:00:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:06:38 (hh:mm:ss) Elapsed Time, 3448 HSPs Collected Number of families returned by RECON: 1028 Round Time: 00:07:33 (hh:mm:ss) Elapsed Time : 7 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 00:01:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12030 repeats masked totaling 3487024 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30775428 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 30011178 bp After Masking: 26019281 bp Masked: 13.30 % -- Input Database Coverage: 40980057 bp out of 591951587 bp ( 6.92 % ) Sampling Time: 00:02:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 296835 Comparison Time: 00:37:34 (hh:mm:ss) Elapsed Time, 30771 HSPs Collected Number of families returned by RECON: 4314 Round Time: 00:40:49 (hh:mm:ss) Elapsed Time : 53 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 41231 repeats masked totaling 11243332 bp(s). - TE Masking time 00:01:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 92056116 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 90003719 bp After Masking: 77510233 bp Masked: 13.88 % -- Input Database Coverage: 133036173 bp out of 591951587 bp ( 22.47 % ) Sampling Time: 00:05:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2673828 Comparison Time: 04:36:48 (hh:mm:ss) Elapsed Time, 198914 HSPs Collected Number of families returned by RECON: 18735 Round Time: 04:54:58 (hh:mm:ss) Elapsed Time : 334 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 179661 repeats masked totaling 45038584 bp(s). - TE Masking time 00:08:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 275901996 bp Num Contigs Represented = 100 Non ambiguous bp: Initial: 270035233 bp After Masking: 221284619 bp Masked: 18.05 % -- Input Database Coverage: 408938169 bp out of 591951587 bp ( 69.08 % ) Sampling Time: 00:21:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24002056 Comparison Time: 35:59:18 (hh:mm:ss) Elapsed Time, 751230 HSPs Collected Number of families returned by RECON: 77189 Round Time: 38:37:34 (hh:mm:ss) Elapsed Time : 842 families discovered. RepeatScout/RECON discovery complete: 1471 families found Classification Time: 01:31:33 (hh:mm:ss) Elapsed Time Program Time: 46:17:01 (hh:mm:ss) Elapsed Time