RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.WlSNYb/RM_25577.SatDec311118582022 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: 1672514337 Database = /dev/shm/rModeler.WlSNYb/GCF_902167405.1_gadMor3.0 - Sequences = 227 - Bases = 669966409 - N50 = 28829685 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 40878493-43798135 | [ 1 ] 37958851-40878492 | [ ] 35039210-37958851 | [ ] 32119568-35039209 | [ 2 ] 29199927-32119568 |* [ 6 ] 26280285-29199926 |* [ 6 ] 23360644-26280285 |* [ 5 ] 20441002-23360643 | [ 3 ] 17521361-20441002 | [ ] 14601719-17521360 | [ ] 11682078-14601719 | [ ] 8762436-11682077 | [ ] 5842795-8762436 | [ ] 2923153-5842794 | [ ] 3512-2923153 |************************************************** [ 204 ] Storage Throughput = excellent ( 1169.49 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 41223880 bp ( 40031037 non ambiguous ) - Num Contigs Represented = 62 - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:37 (hh:mm:ss) Elapsed Time Round Time: 00:34:48 (hh:mm:ss) Elapsed Time : 681 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7509 repeats masked totaling 1544105 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10461702 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10009732 bp After Masking: 7332534 bp Masked: 26.75 % -- Input Database Coverage: 10461702 bp out of 669966409 bp ( 1.56 % ) Sampling Time: 00:02:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 34453 Comparison Time: 00:07:01 (hh:mm:ss) Elapsed Time, 5773 HSPs Collected Number of families returned by RECON: 1165 Round Time: 00:09:39 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 24567 repeats masked totaling 5137136 bp(s). - TE Masking time 00:01:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30762098 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 30021225 bp After Masking: 21506591 bp Masked: 28.36 % -- Input Database Coverage: 41223800 bp out of 669966409 bp ( 6.15 % ) Sampling Time: 00:07:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 299925 Comparison Time: 00:34:52 (hh:mm:ss) Elapsed Time, 41629 HSPs Collected Number of families returned by RECON: 4275 Round Time: 00:43:12 (hh:mm:ss) Elapsed Time : 55 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 76402 repeats masked totaling 15760966 bp(s). - TE Masking time 00:03:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 93729132 bp Num Contigs Represented = 67 Non ambiguous bp: Initial: 90019421 bp After Masking: 65063639 bp Masked: 27.72 % -- Input Database Coverage: 134952932 bp out of 669966409 bp ( 20.14 % ) Sampling Time: 00:19:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2781261 Comparison Time: 04:04:57 (hh:mm:ss) Elapsed Time, 326082 HSPs Collected Number of families returned by RECON: 15077 Round Time: 04:56:54 (hh:mm:ss) Elapsed Time : 513 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:42:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 294191 repeats masked totaling 63314342 bp(s). - TE Masking time 00:19:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 279841415 bp Num Contigs Represented = 160 Non ambiguous bp: Initial: 270016913 bp After Masking: 178385371 bp Masked: 33.94 % -- Input Database Coverage: 414794347 bp out of 669966409 bp ( 61.91 % ) Sampling Time: 01:07:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24819535 Comparison Time: 29:19:28 (hh:mm:ss) Elapsed Time, 996203 HSPs Collected Number of families returned by RECON: 51218 Round Time: 32:06:11 (hh:mm:ss) Elapsed Time : 1252 families discovered. RepeatScout/RECON discovery complete: 2508 families found Classification Time: 02:25:09 (hh:mm:ss) Elapsed Time Program Time: 40:55:53 (hh:mm:ss) Elapsed Time