RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.nciRBa/RM_682162.WedDec40032052024 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: 1733301124 Database = /scratch/tmp/rModeler.nciRBa/GCA_964270875.1_rPodFil1.hap2.1 - Sequences = 142 - Bases = 1404018672 - N50 = 99279823 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 127047298-136122034 | [ 1 ] 117972562-127047297 | [ 2 ] 108897827-117972562 | [ ] 99823091-108897826 | [ 2 ] 90748356-99823091 |* [ 3 ] 81673620-90748355 | [ ] 72598884-81673619 | [ 2 ] 63524149-72598884 | [ ] 54449413-63524148 | [ 2 ] 45374678-54449413 | [ 2 ] 36299942-45374677 |* [ 3 ] 27225206-36299941 | [ ] 18150471-27225206 | [ ] 9075735-18150470 | [ 1 ] 1000-9075735 |************************************************** [ 124 ] Storage Throughput = excellent ( 1572.78 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40011281 bp ( 40006281 non ambiguous ) - Num Contigs Represented = 25 - Sequence extraction : 00:00:54 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:34 (hh:mm:ss) Elapsed Time Round Time: 00:10:09 (hh:mm:ss) Elapsed Time : 539 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 00:00:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17298 repeats masked totaling 2988989 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10036429 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 10034629 bp After Masking: 6784994 bp Masked: 32.38 % -- Input Database Coverage: 10036429 bp out of 1404018672 bp ( 0.71 % ) Sampling Time: 00:00:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:56 (hh:mm:ss) Elapsed Time, 9831 HSPs Collected Number of families returned by RECON: 1343 Round Time: 00:03:39 (hh:mm:ss) Elapsed Time : 23 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 55252 repeats masked totaling 9721830 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30014852 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 30011652 bp After Masking: 19640755 bp Masked: 34.56 % -- Input Database Coverage: 40051281 bp out of 1404018672 bp ( 2.85 % ) Sampling Time: 00:01:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:12:47 (hh:mm:ss) Elapsed Time, 46560 HSPs Collected Number of families returned by RECON: 4375 Round Time: 00:15:14 (hh:mm:ss) Elapsed Time : 126 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 173084 repeats masked totaling 30560478 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90047320 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 90039720 bp After Masking: 57117668 bp Masked: 36.56 % -- Input Database Coverage: 130098601 bp out of 1404018672 bp ( 9.27 % ) Sampling Time: 00:04:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 01:14:13 (hh:mm:ss) Elapsed Time, 205283 HSPs Collected Number of families returned by RECON: 14366 Round Time: 01:24:17 (hh:mm:ss) Elapsed Time : 432 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 590319 repeats masked totaling 103613669 bp(s). - TE Masking time 00:02:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270062215 bp Num Contigs Represented = 59 Non ambiguous bp: Initial: 270030779 bp After Masking: 159457182 bp Masked: 40.95 % -- Input Database Coverage: 400160816 bp out of 1404018672 bp ( 28.50 % ) Sampling Time: 00:13:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22858941 Comparison Time: 08:02:44 (hh:mm:ss) Elapsed Time, 525501 HSPs Collected Number of families returned by RECON: 50860 Round Time: 08:46:18 (hh:mm:ss) Elapsed Time : 1045 families discovered. RepeatScout/RECON discovery complete: 2165 families found Classification Time: 00:31:37 (hh:mm:ss) Elapsed Time Program Time: 11:11:14 (hh:mm:ss) Elapsed Time