RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.nnvte7/RM_12407.TueNov280133412023 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: 1701164016 Database = /dev/shm/rModeler.nnvte7/GCA_027917425.1_aGasCar1.pri - Sequences = 1002 - Bases = 4336248441 - N50 = 525281557 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 616149279-660159871 | [ 2 ] 572138688-616149279 | [ ] 528128096-572138687 | [ ] 484117505-528128096 | [ 2 ] 440106914-484117505 | [ 2 ] 396096322-440106913 | [ ] 352085731-396096322 | [ ] 308075139-352085730 | [ ] 264064548-308075139 | [ 1 ] 220053957-264064548 | [ ] 176043365-220053956 | [ 3 ] 132032774-176043365 | [ 1 ] 88022182-132032773 | [ ] 44011591-88022182 | [ ] 1000-44011591 |************************************************** [ 991 ] Storage Throughput = excellent ( 1203.29 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40038006 bp ( 40036406 non ambiguous ) - Num Contigs Represented = 34 - Sequence extraction : 00:09:27 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:28 (hh:mm:ss) Elapsed Time Round Time: 00:46:13 (hh:mm:ss) Elapsed Time : 829 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:02:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15685 repeats masked totaling 4792943 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10023343 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 10022743 bp After Masking: 3574082 bp Masked: 64.34 % -- Input Database Coverage: 10023343 bp out of 4336248441 bp ( 0.23 % ) Sampling Time: 00:04:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:19 (hh:mm:ss) Elapsed Time, 13566 HSPs Collected Number of families returned by RECON: 1260 Round Time: 00:10:56 (hh:mm:ss) Elapsed Time : 22 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:07:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 50800 repeats masked totaling 15786655 bp(s). - TE Masking time 00:01:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30014583 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30013583 bp After Masking: 10367409 bp Masked: 65.46 % -- Input Database Coverage: 40037926 bp out of 4336248441 bp ( 0.92 % ) Sampling Time: 00:14:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:22:49 (hh:mm:ss) Elapsed Time, 52698 HSPs Collected Number of families returned by RECON: 4023 Round Time: 00:38:39 (hh:mm:ss) Elapsed Time : 128 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:21:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 158827 repeats masked totaling 47901163 bp(s). - TE Masking time 00:03:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90010818 bp Num Contigs Represented = 67 Non ambiguous bp: Initial: 90004018 bp After Masking: 29162410 bp Masked: 67.60 % -- Input Database Coverage: 130048744 bp out of 4336248441 bp ( 3.00 % ) Sampling Time: 00:45:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 01:50:16 (hh:mm:ss) Elapsed Time, 290102 HSPs Collected Number of families returned by RECON: 10769 Round Time: 02:45:44 (hh:mm:ss) Elapsed Time : 471 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:03:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:52:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 545778 repeats masked totaling 159095449 bp(s). - TE Masking time 00:15:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270028083 bp Num Contigs Represented = 153 Non ambiguous bp: Initial: 270006299 bp After Masking: 72936027 bp Masked: 72.99 % -- Input Database Coverage: 400076827 bp out of 4336248441 bp ( 9.23 % ) Sampling Time: 02:11:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22980810 Comparison Time: 11:05:16 (hh:mm:ss) Elapsed Time, 797740 HSPs Collected Number of families returned by RECON: 26571 Round Time: 14:05:29 (hh:mm:ss) Elapsed Time : 1167 families discovered. RepeatScout/RECON discovery complete: 2617 families found Classification Time: 01:44:12 (hh:mm:ss) Elapsed Time Program Time: 20:11:13 (hh:mm:ss) Elapsed Time