RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.LU4v5t/RM_2469.SatMay272054422023 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: 1685246080 Database = /dev/shm/rModeler.LU4v5t/GCF_023898315.1_iqSchNite1.1 - Sequences = 512 - Bases = 8822571301 - N50 = 995565409 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 1238185111-1326626762 | [ 1 ] 1149743460-1238185110 | [ 1 ] 1061301809-1149743459 | [ ] 972860158-1061301808 | [ 2 ] 884418508-972860158 | [ ] 795976857-884418507 | [ 1 ] 707535206-795976856 | [ 1 ] 619093555-707535205 | [ 2 ] 530651904-619093554 | [ 1 ] 442210254-530651904 | [ ] 353768603-442210253 | [ ] 265326952-353768602 | [ ] 176885301-265326951 | [ 3 ] 88443650-176885300 | [ ] 2000-88443650 |************************************************** [ 500 ] Storage Throughput = fair ( 550.26 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40017622 bp ( 40016122 non ambiguous ) - Num Contigs Represented = 28 - Sequence extraction : 00:39:18 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:34:27 (hh:mm:ss) Elapsed Time Round Time: 01:29:06 (hh:mm:ss) Elapsed Time : 798 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:04:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14752 repeats masked totaling 4941920 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10020816 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10020316 bp After Masking: 4472959 bp Masked: 55.36 % -- Input Database Coverage: 10020816 bp out of 8822571301 bp ( 0.11 % ) Sampling Time: 00:05:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:07:32 (hh:mm:ss) Elapsed Time, 24566 HSPs Collected Number of families returned by RECON: 1494 Round Time: 00:14:52 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:13:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43914 repeats masked totaling 15085215 bp(s). - TE Masking time 00:01:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30036726 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 30035726 bp After Masking: 13166695 bp Masked: 56.16 % -- Input Database Coverage: 40057542 bp out of 8822571301 bp ( 0.45 % ) Sampling Time: 00:16:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:30:53 (hh:mm:ss) Elapsed Time, 48904 HSPs Collected Number of families returned by RECON: 5098 Round Time: 00:52:57 (hh:mm:ss) Elapsed Time : 105 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:57:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 137232 repeats masked totaling 46697867 bp(s). - TE Masking time 00:04:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90040981 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 90037981 bp After Masking: 37823515 bp Masked: 57.99 % -- Input Database Coverage: 130098523 bp out of 8822571301 bp ( 1.47 % ) Sampling Time: 01:11:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 02:50:32 (hh:mm:ss) Elapsed Time, 319937 HSPs Collected Number of families returned by RECON: 13665 Round Time: 04:22:06 (hh:mm:ss) Elapsed Time : 619 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 04:28:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:28:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 480865 repeats masked totaling 163205814 bp(s). - TE Masking time 00:21:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270031661 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 270028161 bp After Masking: 91495555 bp Masked: 66.12 % -- Input Database Coverage: 400130184 bp out of 8822571301 bp ( 4.54 % ) Sampling Time: 05:19:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22845420 Comparison Time: 17:15:54 (hh:mm:ss) Elapsed Time, 1009921 HSPs Collected Number of families returned by RECON: 31336 Round Time: 24:09:35 (hh:mm:ss) Elapsed Time : 1790 families discovered. RepeatScout/RECON discovery complete: 3321 families found Classification Time: 08:34:10 (hh:mm:ss) Elapsed Time Program Time: 39:42:46 (hh:mm:ss) Elapsed Time