RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.bNjV4D/RM_3056692.SunDec81358072024 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: 1733695086 Database = /scratch/tmp/rModeler.bNjV4D/GCA_964261635.1_aLisHel1.1 - Sequences = 150 - Bases = 8258219858 - N50 = 2146314909 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 2003227315-2146314909 | [ 2 ] 1860139721-2003227314 | [ 1 ] 1717052127-1860139720 | [ ] 1573964533-1717052126 | [ ] 1430876939-1573964532 | [ ] 1287789345-1430876938 | [ ] 1144701751-1287789344 | [ 1 ] 1001614157-1144701750 | [ ] 858526563-1001614156 | [ ] 715438969-858526562 | [ ] 572351375-715438968 | [ ] 429263781-572351374 | [ 1 ] 286176187-429263780 | [ ] 143088593-286176186 | [ 1 ] 1000-143088593 |************************************************** [ 144 ] Storage Throughput = excellent ( 1423.92 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001785 bp ( 40000385 non ambiguous ) - Num Contigs Represented = 19 - Sequence extraction : 00:18:10 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:05 (hh:mm:ss) Elapsed Time Round Time: 00:32:37 (hh:mm:ss) Elapsed Time : 702 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:04:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10306 repeats masked totaling 4334962 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000716 bp Num Contigs Represented = 12 Non ambiguous bp: Initial: 10000516 bp After Masking: 5118622 bp Masked: 48.82 % -- Input Database Coverage: 10000716 bp out of 8258219858 bp ( 0.12 % ) Sampling Time: 00:05:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:10 (hh:mm:ss) Elapsed Time, 26591 HSPs Collected Number of families returned by RECON: 1442 Round Time: 00:08:45 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:13:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31069 repeats masked totaling 13110958 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30040989 bp Num Contigs Represented = 15 Non ambiguous bp: Initial: 30039789 bp After Masking: 14893652 bp Masked: 50.42 % -- Input Database Coverage: 40041705 bp out of 8258219858 bp ( 0.48 % ) Sampling Time: 00:15:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:11:49 (hh:mm:ss) Elapsed Time, 71749 HSPs Collected Number of families returned by RECON: 4595 Round Time: 00:28:33 (hh:mm:ss) Elapsed Time : 88 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:41:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 99903 repeats masked totaling 42026408 bp(s). - TE Masking time 00:00:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90021073 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 90016473 bp After Masking: 41461346 bp Masked: 53.94 % -- Input Database Coverage: 130062778 bp out of 8258219858 bp ( 1.57 % ) Sampling Time: 00:48:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 00:54:38 (hh:mm:ss) Elapsed Time, 519242 HSPs Collected Number of families returned by RECON: 12802 Round Time: 01:48:45 (hh:mm:ss) Elapsed Time : 460 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 02:02:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 368550 repeats masked totaling 152337590 bp(s). - TE Masking time 00:04:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270042241 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 270028641 bp After Masking: 99240742 bp Masked: 63.25 % -- Input Database Coverage: 400105019 bp out of 8258219858 bp ( 4.84 % ) Sampling Time: 02:25:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22804881 Comparison Time: 04:51:49 (hh:mm:ss) Elapsed Time, 1962326 HSPs Collected Number of families returned by RECON: 34873 Round Time: 07:46:06 (hh:mm:ss) Elapsed Time : 1147 families discovered. RepeatScout/RECON discovery complete: 2405 families found Classification Time: 00:59:34 (hh:mm:ss) Elapsed Time Program Time: 11:44:20 (hh:mm:ss) Elapsed Time