RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.9LUP3v/RM_17788.SunDec80744572024 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: 1733672697 Database = /scratch/tmp/rModeler.9LUP3v/GCA_038501915.1_aXenPet1.maternal.cur - Sequences = 1183 - Bases = 2613116200 - N50 = 149305830 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 221128352-236922605 | [ 1 ] 205334099-221128352 | [ ] 189539846-205334099 | [ ] 173745593-189539846 | [ ] 157951340-173745593 | [ 5 ] 142157087-157951340 | [ 2 ] 126362834-142157087 | [ 3 ] 110568581-126362834 | [ 4 ] 94774328-110568581 | [ 2 ] 78980075-94774328 | [ ] 63185822-78980075 | [ 1 ] 47391569-63185822 | [ ] 31597316-47391569 | [ ] 15803063-31597316 | [ ] 8810-15803063 |************************************************** [ 1165 ] Storage Throughput = fair ( 596.27 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40040347 bp ( 40037147 non ambiguous ) - Num Contigs Represented = 52 - Sequence extraction : 00:03:04 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:27 (hh:mm:ss) Elapsed Time Round Time: 00:31:26 (hh:mm:ss) Elapsed Time : 673 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18574 repeats masked totaling 3550049 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10038594 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10037994 bp After Masking: 5963673 bp Masked: 40.59 % -- Input Database Coverage: 10038594 bp out of 2613116200 bp ( 0.38 % ) Sampling Time: 00:01:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:05:23 (hh:mm:ss) Elapsed Time, 11603 HSPs Collected Number of families returned by RECON: 1252 Round Time: 00:07:48 (hh:mm:ss) Elapsed Time : 27 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 56512 repeats masked totaling 10832965 bp(s). - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30041597 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 30038997 bp After Masking: 17521808 bp Masked: 41.67 % -- Input Database Coverage: 40080191 bp out of 2613116200 bp ( 1.53 % ) Sampling Time: 00:05:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:26:41 (hh:mm:ss) Elapsed Time, 85628 HSPs Collected Number of families returned by RECON: 4115 Round Time: 00:35:58 (hh:mm:ss) Elapsed Time : 106 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 179361 repeats masked totaling 35093795 bp(s). - TE Masking time 00:02:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90030764 bp Num Contigs Represented = 104 Non ambiguous bp: Initial: 90023564 bp After Masking: 50062000 bp Masked: 44.39 % -- Input Database Coverage: 130110955 bp out of 2613116200 bp ( 4.98 % ) Sampling Time: 00:17:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2582128 Comparison Time: 02:54:49 (hh:mm:ss) Elapsed Time, 714071 HSPs Collected Number of families returned by RECON: 13506 Round Time: 03:41:02 (hh:mm:ss) Elapsed Time : 388 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:21:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 595765 repeats masked totaling 115959730 bp(s). - TE Masking time 00:10:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270046017 bp Num Contigs Represented = 250 Non ambiguous bp: Initial: 270025417 bp After Masking: 139300152 bp Masked: 48.41 % -- Input Database Coverage: 400156972 bp out of 2613116200 bp ( 15.31 % ) Sampling Time: 00:55:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23130201 Comparison Time: 21:49:22 (hh:mm:ss) Elapsed Time, 787554 HSPs Collected Number of families returned by RECON: 46369 Round Time: 25:04:52 (hh:mm:ss) Elapsed Time : 1126 families discovered. RepeatScout/RECON discovery complete: 2320 families found Classification Time: 01:30:16 (hh:mm:ss) Elapsed Time Program Time: 31:31:22 (hh:mm:ss) Elapsed Time