RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.gHMMae/RM_21300.WedJan101934582024 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: 1704944097 Database = /dev/shm/rModeler.gHMMae/GCA_012275275.1_bMelUnd1.pat - Sequences = 330 - Bases = 1124753724 - N50 = 112710647 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 225493021-241599620 | [ 1 ] 209386423-225493021 | [ ] 193279825-209386423 | [ ] 177173226-193279824 | [ ] 161066628-177173226 | [ ] 144960030-161066628 | [ ] 128853431-144960029 | [ ] 112746833-128853431 | [ 1 ] 96640235-112746833 | [ 2 ] 80533636-96640234 | [ 2 ] 64427038-80533636 | [ ] 48320440-64427038 | [ 2 ] 32213841-48320439 | [ 2 ] 16107243-32213841 | [ 2 ] 645-16107243 |************************************************** [ 318 ] Storage Throughput = excellent ( 1124.08 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40435763 bp ( 40034919 non ambiguous ) - Num Contigs Represented = 55 - Sequence extraction : 00:02:21 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:26 (hh:mm:ss) Elapsed Time Round Time: 00:27:34 (hh:mm:ss) Elapsed Time : 72 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2780 repeats masked totaling 829656 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10121382 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10002683 bp After Masking: 8984713 bp Masked: 10.18 % -- Input Database Coverage: 10121382 bp out of 1124753724 bp ( 0.90 % ) Sampling Time: 00:01:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:57 (hh:mm:ss) Elapsed Time, 423 HSPs Collected Number of families returned by RECON: 193 Round Time: 00:07:11 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8665 repeats masked totaling 2507313 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30314301 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 30032156 bp After Masking: 27124083 bp Masked: 9.68 % -- Input Database Coverage: 40435683 bp out of 1124753724 bp ( 3.60 % ) Sampling Time: 00:03:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289180 Comparison Time: 00:34:40 (hh:mm:ss) Elapsed Time, 2902 HSPs Collected Number of families returned by RECON: 1332 Round Time: 00:38:07 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26393 repeats masked totaling 7822815 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90920204 bp Num Contigs Represented = 90 Non ambiguous bp: Initial: 90038743 bp After Masking: 80955147 bp Masked: 10.09 % -- Input Database Coverage: 131355887 bp out of 1124753724 bp ( 11.68 % ) Sampling Time: 00:10:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2620905 Comparison Time: 04:26:01 (hh:mm:ss) Elapsed Time, 42866 HSPs Collected Number of families returned by RECON: 9309 Round Time: 04:39:03 (hh:mm:ss) Elapsed Time : 52 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 84692 repeats masked totaling 24889530 bp(s). - TE Masking time 00:02:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272968507 bp Num Contigs Represented = 163 Non ambiguous bp: Initial: 270030179 bp After Masking: 240940400 bp Masked: 10.77 % -- Input Database Coverage: 404324394 bp out of 1124753724 bp ( 35.95 % ) Sampling Time: 00:35:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23546953 Comparison Time: 39:46:03 (hh:mm:ss) Elapsed Time, 156584 HSPs Collected Number of families returned by RECON: 63531 Round Time: 41:21:52 (hh:mm:ss) Elapsed Time : 186 families discovered. RepeatScout/RECON discovery complete: 315 families found Classification Time: 00:34:37 (hh:mm:ss) Elapsed Time Program Time: 47:48:24 (hh:mm:ss) Elapsed Time