RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.gio3ar/RM_159702.MonJan21538492023 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: 1672702728 Database = /dev/shm/rModeler.gio3ar/GCF_900747795.1_fErpCal1.1 - Sequences = 1885 - Bases = 3811038701 - N50 = 209933285 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 326758906-350098611 | [ 2 ] 303419201-326758905 | [ 1 ] 280079497-303419201 | [ 1 ] 256739792-280079496 | [ ] 233400088-256739792 | [ ] 210060383-233400087 | [ 1 ] 186720678-210060382 | [ 4 ] 163380974-186720678 | [ 3 ] 140041269-163380973 | [ 1 ] 116701565-140041269 | [ ] 93361860-116701564 | [ 4 ] 70022155-93361859 | [ 1 ] 46682451-70022155 | [ ] 23342746-46682450 | [ ] 3042-23342746 |************************************************* [ 1867 ] Storage Throughput = excellent ( 1447.89 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 42508738 bp ( 40005554 non ambiguous ) - Num Contigs Represented = 107 - Sequence extraction : 00:05:01 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:38 (hh:mm:ss) Elapsed Time Round Time: 00:32:56 (hh:mm:ss) Elapsed Time : 835 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17057 repeats masked totaling 4550133 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10714363 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 10030790 bp After Masking: 5326406 bp Masked: 46.90 % -- Input Database Coverage: 10714363 bp out of 3811038701 bp ( 0.28 % ) Sampling Time: 00:02:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 36585 Comparison Time: 00:05:50 (hh:mm:ss) Elapsed Time, 8553 HSPs Collected Number of families returned by RECON: 1502 Round Time: 00:08:46 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:04:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 50839 repeats masked totaling 13495661 bp(s). - TE Masking time 00:00:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 31834295 bp Num Contigs Represented = 82 Non ambiguous bp: Initial: 30014684 bp After Masking: 16007123 bp Masked: 46.67 % -- Input Database Coverage: 42548658 bp out of 3811038701 bp ( 1.12 % ) Sampling Time: 00:07:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 324415 Comparison Time: 00:25:11 (hh:mm:ss) Elapsed Time, 60513 HSPs Collected Number of families returned by RECON: 4647 Round Time: 00:34:10 (hh:mm:ss) Elapsed Time : 144 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:11:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 167661 repeats masked totaling 44580453 bp(s). - TE Masking time 00:02:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 96053372 bp Num Contigs Represented = 192 Non ambiguous bp: Initial: 90036635 bp After Masking: 44022354 bp Masked: 51.11 % -- Input Database Coverage: 138602030 bp out of 3811038701 bp ( 3.64 % ) Sampling Time: 00:17:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2931831 Comparison Time: 02:32:47 (hh:mm:ss) Elapsed Time, 277578 HSPs Collected Number of families returned by RECON: 11890 Round Time: 03:05:41 (hh:mm:ss) Elapsed Time : 560 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:34:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 581518 repeats masked totaling 151092931 bp(s). - TE Masking time 00:15:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 288962182 bp Num Contigs Represented = 436 Non ambiguous bp: Initial: 270011445 bp After Masking: 114623133 bp Masked: 57.55 % -- Input Database Coverage: 427564212 bp out of 3811038701 bp ( 11.22 % ) Sampling Time: 01:05:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 26604865 Comparison Time: 16:41:32 (hh:mm:ss) Elapsed Time, 636306 HSPs Collected Number of families returned by RECON: 32943 Round Time: 18:33:11 (hh:mm:ss) Elapsed Time : 1238 families discovered. RepeatScout/RECON discovery complete: 2790 families found Classification Time: 01:54:24 (hh:mm:ss) Elapsed Time Program Time: 24:49:08 (hh:mm:ss) Elapsed Time