RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.VpXfnJ/RM_2089660.SunApr131333592025 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: 1744576439 Database = /data/tmp/rModeler.VpXfnJ/GCA_045364815.1_rPodExp1_haplotype_2 - Sequences = 725 - Bases = 2565358608 - N50 = 314527028 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 406471288-435504880 | [ 2 ] 377437696-406471288 | [ ] 348404104-377437696 | [ ] 319370512-348404104 | [ ] 290336920-319370512 | [ 2 ] 261303328-290336920 | [ 1 ] 232269736-261303328 | [ ] 203236144-232269736 | [ ] 174202552-203236144 | [ ] 145168960-174202552 | [ ] 116135368-145168960 | [ 1 ] 87101776-116135368 | [ 2 ] 58068184-87101776 | [ 3 ] 29034592-58068184 | [ 2 ] 1000-29034592 |************************************************** [ 712 ] Storage Throughput = excellent ( 1384.57 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40008900 bp ( 40008100 non ambiguous ) - Num Contigs Represented = 55 - Sequence extraction : 00:02:57 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:08 (hh:mm:ss) Elapsed Time Round Time: 00:20:21 (hh:mm:ss) Elapsed Time : 512 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14478 repeats masked totaling 3310099 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10012707 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 10012707 bp After Masking: 6455223 bp Masked: 35.53 % -- Input Database Coverage: 10012707 bp out of 2565358608 bp ( 0.39 % ) Sampling Time: 00:02:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:03:18 (hh:mm:ss) Elapsed Time, 10377 HSPs Collected Number of families returned by RECON: 1395 Round Time: 00:05:39 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 45786 repeats masked totaling 10247954 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30036113 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 30035313 bp After Masking: 19009656 bp Masked: 36.71 % -- Input Database Coverage: 40048820 bp out of 2565358608 bp ( 1.56 % ) Sampling Time: 00:06:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:14:50 (hh:mm:ss) Elapsed Time, 54010 HSPs Collected Number of families returned by RECON: 4190 Round Time: 00:21:51 (hh:mm:ss) Elapsed Time : 115 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 152262 repeats masked totaling 33255885 bp(s). - TE Masking time 00:01:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90003245 bp Num Contigs Represented = 110 Non ambiguous bp: Initial: 90002045 bp After Masking: 53646558 bp Masked: 40.39 % -- Input Database Coverage: 130052065 bp out of 2565358608 bp ( 5.07 % ) Sampling Time: 00:20:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2561716 Comparison Time: 01:22:42 (hh:mm:ss) Elapsed Time, 219484 HSPs Collected Number of families returned by RECON: 12054 Round Time: 01:46:35 (hh:mm:ss) Elapsed Time : 418 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:16:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:35:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 528117 repeats masked totaling 115723945 bp(s). - TE Masking time 00:05:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270014071 bp Num Contigs Represented = 239 Non ambiguous bp: Initial: 270010671 bp After Masking: 144706478 bp Masked: 46.41 % -- Input Database Coverage: 400066136 bp out of 2565358608 bp ( 15.59 % ) Sampling Time: 00:57:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23041866 Comparison Time: 10:23:07 (hh:mm:ss) Elapsed Time, 662329 HSPs Collected Number of families returned by RECON: 36779 Round Time: 11:51:07 (hh:mm:ss) Elapsed Time : 864 families discovered. RepeatScout/RECON discovery complete: 1929 families found Classification Time: 00:52:20 (hh:mm:ss) Elapsed Time Program Time: 15:17:53 (hh:mm:ss) Elapsed Time