RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.yOKudt/RM_18428.TueJan160245072024 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: 1705401903 Database = /dev/shm/rModeler.yOKudt/GCA_963457625.1_fCycLum2.1 - Sequences = 232 - Bases = 586296809 - N50 = 25165805 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 30161796-32316139 | [ 1 ] 28007453-30161795 | [ 2 ] 25853111-28007453 |* [ 6 ] 23698768-25853110 | [ 4 ] 21544426-23698768 |* [ 5 ] 19390083-21544425 | [ 2 ] 17235740-19390082 | [ 1 ] 15081398-17235740 | [ 2 ] 12927055-15081397 | [ 1 ] 10772713-12927055 | [ 1 ] 8618370-10772712 | [ ] 6464027-8618369 | [ ] 4309685-6464027 | [ ] 2155342-4309684 | [ ] 1000-2155342 |************************************************** [ 207 ] Storage Throughput = excellent ( 1047.74 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40012061 bp ( 40000661 non ambiguous ) - Num Contigs Represented = 38 - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:50 (hh:mm:ss) Elapsed Time Round Time: 00:30:32 (hh:mm:ss) Elapsed Time : 282 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4066 repeats masked totaling 785182 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003679 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10001679 bp After Masking: 8114336 bp Masked: 18.87 % -- Input Database Coverage: 10003679 bp out of 586296809 bp ( 1.71 % ) Sampling Time: 00:02:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:08:04 (hh:mm:ss) Elapsed Time, 7238 HSPs Collected Number of families returned by RECON: 1322 Round Time: 00:11:14 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13566 repeats masked totaling 2553121 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30048366 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 30038966 bp After Masking: 23978979 bp Masked: 20.17 % -- Input Database Coverage: 40052045 bp out of 586296809 bp ( 6.83 % ) Sampling Time: 00:07:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:37:38 (hh:mm:ss) Elapsed Time, 39057 HSPs Collected Number of families returned by RECON: 4692 Round Time: 00:47:11 (hh:mm:ss) Elapsed Time : 73 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46156 repeats masked totaling 8392100 bp(s). - TE Masking time 00:01:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90069063 bp Num Contigs Represented = 64 Non ambiguous bp: Initial: 90035863 bp After Masking: 70911809 bp Masked: 21.24 % -- Input Database Coverage: 130121108 bp out of 586296809 bp ( 22.19 % ) Sampling Time: 00:24:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2584401 Comparison Time: 04:03:48 (hh:mm:ss) Elapsed Time, 249072 HSPs Collected Number of families returned by RECON: 17997 Round Time: 04:52:35 (hh:mm:ss) Elapsed Time : 345 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:04:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 190932 repeats masked totaling 36534359 bp(s). - TE Masking time 00:07:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270090542 bp Num Contigs Represented = 133 Non ambiguous bp: Initial: 270000811 bp After Masking: 202124620 bp Masked: 25.14 % -- Input Database Coverage: 400211650 bp out of 586296809 bp ( 68.26 % ) Sampling Time: 01:16:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23225520 Comparison Time: 31:46:49 (hh:mm:ss) Elapsed Time, 870570 HSPs Collected Number of families returned by RECON: 68618 Round Time: 34:59:25 (hh:mm:ss) Elapsed Time : 856 families discovered. RepeatScout/RECON discovery complete: 1571 families found Classification Time: 01:18:21 (hh:mm:ss) Elapsed Time Program Time: 42:39:18 (hh:mm:ss) Elapsed Time