RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.ZI7189/RM_1907646.SatNov161520062024 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: 1731799206 Database = /scratch/tmp/rModeler.ZI7189/GCA_963455315.2_mGloMel1.2 - Sequences = 993 - Bases = 2651292441 - N50 = 108122213 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 175565434-188105751 | [ 2 ] 163025117-175565433 | [ 1 ] 150484800-163025116 | [ ] 137944484-150484800 | [ 2 ] 125404167-137944483 | [ 1 ] 112863850-125404166 | [ 2 ] 100323533-112863849 | [ 4 ] 87783217-100323533 | [ 3 ] 75242900-87783216 | [ 4 ] 62702583-75242899 | [ 1 ] 50162266-62702582 | [ 1 ] 37621950-50162266 | [ ] 25081633-37621949 | [ 1 ] 12541316-25081632 | [ ] 1000-12541316 |************************************************* [ 971 ] Storage Throughput = excellent ( 1403.64 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40038098 bp ( 40034098 non ambiguous ) - Num Contigs Represented = 123 - Sequence extraction : 00:01:10 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:34 (hh:mm:ss) Elapsed Time Round Time: 00:15:39 (hh:mm:ss) Elapsed Time : 189 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:17 (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... 8972 repeats masked totaling 2700684 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027182 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 10026182 bp After Masking: 6921754 bp Masked: 30.96 % -- Input Database Coverage: 10027182 bp out of 2651292441 bp ( 0.38 % ) Sampling Time: 00:00:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:03:33 (hh:mm:ss) Elapsed Time, 12710 HSPs Collected Number of families returned by RECON: 894 Round Time: 00:04:34 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31126 repeats masked totaling 9734920 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30010912 bp Num Contigs Represented = 104 Non ambiguous bp: Initial: 30007912 bp After Masking: 19120730 bp Masked: 36.28 % -- Input Database Coverage: 40038094 bp out of 2651292441 bp ( 1.51 % ) Sampling Time: 00:02:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:15:08 (hh:mm:ss) Elapsed Time, 47691 HSPs Collected Number of families returned by RECON: 2613 Round Time: 00:18:29 (hh:mm:ss) Elapsed Time : 76 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 103435 repeats masked totaling 31864217 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90028012 bp Num Contigs Represented = 228 Non ambiguous bp: Initial: 90021812 bp After Masking: 55259091 bp Masked: 38.62 % -- Input Database Coverage: 130066106 bp out of 2651292441 bp ( 4.91 % ) Sampling Time: 00:06:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2584401 Comparison Time: 01:37:10 (hh:mm:ss) Elapsed Time, 609089 HSPs Collected Number of families returned by RECON: 8467 Round Time: 01:46:03 (hh:mm:ss) Elapsed Time : 164 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 354805 repeats masked totaling 103587229 bp(s). - TE Masking time 00:01:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270046006 bp Num Contigs Represented = 423 Non ambiguous bp: Initial: 270027406 bp After Masking: 158226503 bp Masked: 41.40 % -- Input Database Coverage: 400112112 bp out of 2651292441 bp ( 15.09 % ) Sampling Time: 00:19:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23089410 Comparison Time: 08:32:43 (hh:mm:ss) Elapsed Time, 3228739 HSPs Collected Number of families returned by RECON: 31166 Round Time: 09:01:28 (hh:mm:ss) Elapsed Time : 362 families discovered. RepeatScout/RECON discovery complete: 804 families found Classification Time: 00:12:49 (hh:mm:ss) Elapsed Time Program Time: 11:39:02 (hh:mm:ss) Elapsed Time