RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.7rgnTQ/RM_1396329.FriNov150006372024 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: 1731657997 Database = /scratch/tmp/rModeler.7rgnTQ/GCA_964198595.1_kcLamFluv1.1 - Sequences = 1497 - Bases = 1042475189 - N50 = 13477503 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 38858520-41634058 | [ 1 ] 36082983-38858520 | [ 1 ] 33307446-36082983 | [ 1 ] 30531909-33307446 | [ 1 ] 27756372-30531909 | [ ] 24980834-27756371 | [ ] 22205297-24980834 | [ 1 ] 19429760-22205297 | [ ] 16654223-19429760 | [ 2 ] 13878686-16654223 | [ 14 ] 11103148-13878685 | [ 21 ] 8327611-11103148 | [ 17 ] 5552074-8327611 | [ 12 ] 2776537-5552074 | [ 7 ] 1000-2776537 |************************************************** [ 1419 ] Storage Throughput = excellent ( 1513.43 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40021818 bp ( 40007018 non ambiguous ) - Num Contigs Represented = 166 - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:47 (hh:mm:ss) Elapsed Time Round Time: 00:15:28 (hh:mm:ss) Elapsed Time : 574 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 25981 repeats masked totaling 3460580 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10019055 bp Num Contigs Represented = 95 Non ambiguous bp: Initial: 10016055 bp After Masking: 4897058 bp Masked: 51.11 % -- Input Database Coverage: 10019055 bp out of 1042475189 bp ( 0.96 % ) Sampling Time: 00:03:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32896 Comparison Time: 00:02:59 (hh:mm:ss) Elapsed Time, 46334 HSPs Collected Number of families returned by RECON: 1115 Round Time: 00:08:56 (hh:mm:ss) Elapsed Time : 30 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 76514 repeats masked totaling 10553282 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30026763 bp Num Contigs Represented = 149 Non ambiguous bp: Initial: 30014963 bp After Masking: 13464981 bp Masked: 55.14 % -- Input Database Coverage: 40045818 bp out of 1042475189 bp ( 3.84 % ) Sampling Time: 00:14:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 297606 Comparison Time: 00:11:21 (hh:mm:ss) Elapsed Time, 30660 HSPs Collected Number of families returned by RECON: 2892 Round Time: 00:26:06 (hh:mm:ss) Elapsed Time : 97 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:38:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 244537 repeats masked totaling 34157753 bp(s). - TE Masking time 00:00:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90053917 bp Num Contigs Represented = 291 Non ambiguous bp: Initial: 90018917 bp After Masking: 40079646 bp Masked: 55.48 % -- Input Database Coverage: 130099735 bp out of 1042475189 bp ( 12.48 % ) Sampling Time: 00:39:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2727280 Comparison Time: 01:00:36 (hh:mm:ss) Elapsed Time, 150842 HSPs Collected Number of families returned by RECON: 9058 Round Time: 01:46:03 (hh:mm:ss) Elapsed Time : 317 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:57:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 784363 repeats masked totaling 113046482 bp(s). - TE Masking time 00:03:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270123133 bp Num Contigs Represented = 600 Non ambiguous bp: Initial: 270029745 bp After Masking: 109424402 bp Masked: 59.48 % -- Input Database Coverage: 400222868 bp out of 1042475189 bp ( 38.39 % ) Sampling Time: 02:02:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24140826 Comparison Time: 06:13:42 (hh:mm:ss) Elapsed Time, 410019 HSPs Collected Number of families returned by RECON: 28733 Round Time: 08:28:35 (hh:mm:ss) Elapsed Time : 738 families discovered. RepeatScout/RECON discovery complete: 1756 families found Classification Time: 00:26:14 (hh:mm:ss) Elapsed Time Program Time: 11:31:22 (hh:mm:ss) Elapsed Time