RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Fc8bwV/RM_51663.TueJan31559022023 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: 1672790342 Database = /dev/shm/rModeler.Fc8bwV/GCF_013368585.1_fMegCyp1.pri - Sequences = 207 - Bases = 959258046 - N50 = 39133747 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 69082274-74015632 | [ 2 ] 64148916-69082274 | [ ] 59215558-64148916 | [ ] 54282200-59215558 | [ 1 ] 49348842-54282200 | [ ] 44415484-49348842 | [ 1 ] 39482126-44415484 |* [ 4 ] 34548768-39482126 |* [ 6 ] 29615410-34548768 |* [ 5 ] 24682052-29615410 |* [ 4 ] 19748694-24682052 | [ 2 ] 14815336-19748694 | [ ] 9881978-14815336 | [ ] 4948620-9881978 | [ ] 15262-4948620 |************************************************** [ 182 ] Storage Throughput = excellent ( 1045.35 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40037141 bp ( 40036641 non ambiguous ) - Num Contigs Represented = 32 - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:47 (hh:mm:ss) Elapsed Time Round Time: 00:20:05 (hh:mm:ss) Elapsed Time : 175 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3561 repeats masked totaling 635546 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001538 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10001538 bp After Masking: 9124126 bp Masked: 8.77 % -- Input Database Coverage: 10001538 bp out of 959258046 bp ( 1.04 % ) Sampling Time: 00:00:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:09 (hh:mm:ss) Elapsed Time, 3895 HSPs Collected Number of families returned by RECON: 1002 Round Time: 00:07:17 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:36 (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... 10584 repeats masked totaling 1808305 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30035523 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 30035023 bp After Masking: 27281283 bp Masked: 9.17 % -- Input Database Coverage: 40037061 bp out of 959258046 bp ( 4.17 % ) Sampling Time: 00:03:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:31:07 (hh:mm:ss) Elapsed Time, 26155 HSPs Collected Number of families returned by RECON: 4193 Round Time: 00:35:10 (hh:mm:ss) Elapsed Time : 53 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 38036 repeats masked totaling 6809973 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90097970 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 90021200 bp After Masking: 79808450 bp Masked: 11.34 % -- Input Database Coverage: 130135031 bp out of 959258046 bp ( 13.57 % ) Sampling Time: 00:09:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2561716 Comparison Time: 03:15:21 (hh:mm:ss) Elapsed Time, 183424 HSPs Collected Number of families returned by RECON: 17033 Round Time: 03:33:19 (hh:mm:ss) Elapsed Time : 298 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 158035 repeats masked totaling 29839216 bp(s). - TE Masking time 00:04:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270095161 bp Num Contigs Represented = 92 Non ambiguous bp: Initial: 270008874 bp After Masking: 231189551 bp Masked: 14.38 % -- Input Database Coverage: 400230192 bp out of 959258046 bp ( 41.72 % ) Sampling Time: 00:29:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22933378 Comparison Time: 27:42:40 (hh:mm:ss) Elapsed Time, 554104 HSPs Collected Number of families returned by RECON: 73621 Round Time: 30:22:05 (hh:mm:ss) Elapsed Time : 808 families discovered. RepeatScout/RECON discovery complete: 1340 families found Classification Time: 01:10:46 (hh:mm:ss) Elapsed Time Program Time: 36:08:42 (hh:mm:ss) Elapsed Time