RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.oybU8E/RM_1744619.MonNov181537322024 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: 1731973052 Database = /scratch/tmp/rModeler.oybU8E/GCF_035084215.1_sHepPer1.hap1 - Sequences = 1879 - Bases = 3249915908 - N50 = 73985925 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 185325645-198562713 | [ 1 ] 172088577-185325644 | [ 1 ] 158851509-172088576 | [ ] 145614441-158851508 | [ ] 132377373-145614440 | [ 3 ] 119140305-132377372 | [ ] 105903237-119140304 | [ 1 ] 92666169-105903236 | [ 1 ] 79429101-92666168 | [ 4 ] 66192033-79429100 | [ 5 ] 52954965-66192032 | [ 5 ] 39717897-52954964 | [ 7 ] 26480829-39717896 | [ 9 ] 13243761-26480828 | [ 6 ] 6694-13243761 |************************************************** [ 1836 ] Storage Throughput = excellent ( 1526.22 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40005985 bp ( 40002315 non ambiguous ) - Num Contigs Represented = 157 - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:47 (hh:mm:ss) Elapsed Time Round Time: 00:13:23 (hh:mm:ss) Elapsed Time : 362 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:12 (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... 13299 repeats masked totaling 4459559 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10032058 bp Num Contigs Represented = 77 Non ambiguous bp: Initial: 10031258 bp After Masking: 3818469 bp Masked: 61.93 % -- Input Database Coverage: 10032058 bp out of 3249915908 bp ( 0.31 % ) Sampling Time: 00:04:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:02:36 (hh:mm:ss) Elapsed Time, 6983 HSPs Collected Number of families returned by RECON: 923 Round Time: 00:06:53 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 42033 repeats masked totaling 13840234 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30013927 bp Num Contigs Represented = 132 Non ambiguous bp: Initial: 30011057 bp After Masking: 11102849 bp Masked: 63.00 % -- Input Database Coverage: 40045985 bp out of 3249915908 bp ( 1.23 % ) Sampling Time: 00:09:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289180 Comparison Time: 00:09:44 (hh:mm:ss) Elapsed Time, 35437 HSPs Collected Number of families returned by RECON: 3035 Round Time: 00:20:48 (hh:mm:ss) Elapsed Time : 95 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 140711 repeats masked totaling 44619761 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90018603 bp Num Contigs Represented = 264 Non ambiguous bp: Initial: 90008252 bp After Masking: 30380816 bp Masked: 66.25 % -- Input Database Coverage: 130064588 bp out of 3249915908 bp ( 4.00 % ) Sampling Time: 00:27:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2593503 Comparison Time: 00:43:40 (hh:mm:ss) Elapsed Time, 134782 HSPs Collected Number of families returned by RECON: 7733 Round Time: 01:14:16 (hh:mm:ss) Elapsed Time : 282 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:26:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 465254 repeats masked totaling 141379751 bp(s). - TE Masking time 00:02:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270055950 bp Num Contigs Represented = 531 Non ambiguous bp: Initial: 270024350 bp After Masking: 82301642 bp Masked: 69.52 % -- Input Database Coverage: 400120538 bp out of 3249915908 bp ( 12.31 % ) Sampling Time: 01:34:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23300551 Comparison Time: 04:16:54 (hh:mm:ss) Elapsed Time, 375981 HSPs Collected Number of families returned by RECON: 22056 Round Time: 06:02:00 (hh:mm:ss) Elapsed Time : 715 families discovered. RepeatScout/RECON discovery complete: 1471 families found Classification Time: 00:28:13 (hh:mm:ss) Elapsed Time Program Time: 08:25:33 (hh:mm:ss) Elapsed Time