RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.NriusD/RM_22523.FriDec80905452023 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: 1702055144 Database = /dev/shm/rModeler.NriusD/GCA_951216825.1_fEleAnt2.1 - Sequences = 1901 - Bases = 1427445741 - N50 = 54824592 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 61343522-65725131 | [ 4 ] 56961913-61343521 | [ 5 ] 52580304-56961912 | [ 3 ] 48198696-52580304 | [ 5 ] 43817087-48198695 | [ 2 ] 39435478-43817086 | [ 4 ] 35053869-39435477 | [ ] 30672261-35053869 | [ 1 ] 26290652-30672260 | [ ] 21909043-26290651 | [ ] 17527434-21909042 | [ ] 13145826-17527434 | [ ] 8764217-13145825 | [ 1 ] 4382608-8764216 | [ ] 1000-4382608 |************************************************* [ 1876 ] Storage Throughput = excellent ( 1118.38 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40031304 bp ( 40012295 non ambiguous ) - Num Contigs Represented = 147 - Sequence extraction : 00:01:01 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:35 (hh:mm:ss) Elapsed Time Round Time: 00:47:45 (hh:mm:ss) Elapsed Time : 1254 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23415 repeats masked totaling 3170082 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10017106 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 10011897 bp After Masking: 5043276 bp Masked: 49.63 % -- Input Database Coverage: 10017106 bp out of 1427445741 bp ( 0.70 % ) Sampling Time: 00:02:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:05:30 (hh:mm:ss) Elapsed Time, 12276 HSPs Collected Number of families returned by RECON: 1546 Round Time: 00:08:25 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 73785 repeats masked totaling 9994898 bp(s). - TE Masking time 00:01:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30014118 bp Num Contigs Represented = 120 Non ambiguous bp: Initial: 30000318 bp After Masking: 15215058 bp Masked: 49.28 % -- Input Database Coverage: 40031224 bp out of 1427445741 bp ( 2.80 % ) Sampling Time: 00:06:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 299925 Comparison Time: 00:25:41 (hh:mm:ss) Elapsed Time, 58542 HSPs Collected Number of families returned by RECON: 5615 Round Time: 00:34:59 (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 : 00:02:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 228128 repeats masked totaling 29935495 bp(s). - TE Masking time 00:03:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90042271 bp Num Contigs Represented = 255 Non ambiguous bp: Initial: 90004071 bp After Masking: 44370570 bp Masked: 50.70 % -- Input Database Coverage: 130073495 bp out of 1427445741 bp ( 9.11 % ) Sampling Time: 00:24:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2646150 Comparison Time: 02:40:18 (hh:mm:ss) Elapsed Time, 442069 HSPs Collected Number of families returned by RECON: 16734 Round Time: 03:26:26 (hh:mm:ss) Elapsed Time : 750 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:52:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 756583 repeats masked totaling 104951844 bp(s). - TE Masking time 00:17:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270146034 bp Num Contigs Represented = 649 Non ambiguous bp: Initial: 270030099 bp After Masking: 117090306 bp Masked: 56.64 % -- Input Database Coverage: 400219529 bp out of 1427445741 bp ( 28.04 % ) Sampling Time: 01:17:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24210361 Comparison Time: 17:39:47 (hh:mm:ss) Elapsed Time, 1098575 HSPs Collected Number of families returned by RECON: 48671 Round Time: 20:55:21 (hh:mm:ss) Elapsed Time : 1731 families discovered. RepeatScout/RECON discovery complete: 3873 families found Classification Time: 02:26:20 (hh:mm:ss) Elapsed Time Program Time: 28:19:16 (hh:mm:ss) Elapsed Time