RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.wt2DpX/RM_982748.TueMar120311302024 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: 1710238289 Database = /dev/shm/rModeler.wt2DpX/GCA_035046495.1_rTilSci1.hap1 - Sequences = 827 - Bases = 1694434935 - N50 = 282992794 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 293863556-314852809 | [ 1 ] 272874303-293863555 | [ 1 ] 251885050-272874302 | [ ] 230895797-251885049 | [ 1 ] 209906544-230895796 | [ 1 ] 188917291-209906543 | [ ] 167928038-188917290 | [ ] 146938785-167928037 | [ 1 ] 125949532-146938784 | [ ] 104960279-125949531 | [ ] 83971026-104960278 | [ 1 ] 62981773-83971025 | [ 1 ] 41992520-62981772 | [ 2 ] 21003267-41992519 | [ 5 ] 14015-21003267 |************************************************* [ 813 ] Storage Throughput = excellent ( 1426.09 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40024761 bp ( 40023961 non ambiguous ) - Num Contigs Represented = 43 - Sequence extraction : 00:03:58 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:09 (hh:mm:ss) Elapsed Time Round Time: 00:24:56 (hh:mm:ss) Elapsed Time : 544 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19077 repeats masked totaling 3465723 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10010828 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 10010228 bp After Masking: 6335567 bp Masked: 36.71 % -- Input Database Coverage: 10010828 bp out of 1694434935 bp ( 0.59 % ) Sampling Time: 00:02:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:25 (hh:mm:ss) Elapsed Time, 9626 HSPs Collected Number of families returned by RECON: 1273 Round Time: 00:08:00 (hh:mm:ss) Elapsed Time : 26 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 61350 repeats masked totaling 11095530 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30013907 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 30013707 bp After Masking: 18463575 bp Masked: 38.48 % -- Input Database Coverage: 40024735 bp out of 1694434935 bp ( 2.36 % ) Sampling Time: 00:04:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:25:43 (hh:mm:ss) Elapsed Time, 45861 HSPs Collected Number of families returned by RECON: 4324 Round Time: 00:31:57 (hh:mm:ss) Elapsed Time : 119 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:09:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 199501 repeats masked totaling 35835216 bp(s). - TE Masking time 00:01:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90033956 bp Num Contigs Represented = 69 Non ambiguous bp: Initial: 90030865 bp After Masking: 52867820 bp Masked: 41.28 % -- Input Database Coverage: 130058691 bp out of 1694434935 bp ( 7.68 % ) Sampling Time: 00:13:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2575315 Comparison Time: 02:51:32 (hh:mm:ss) Elapsed Time, 219318 HSPs Collected Number of families returned by RECON: 13412 Round Time: 03:16:58 (hh:mm:ss) Elapsed Time : 417 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:28:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 663567 repeats masked totaling 118652204 bp(s). - TE Masking time 00:08:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270028050 bp Num Contigs Represented = 178 Non ambiguous bp: Initial: 270019050 bp After Masking: 147427158 bp Masked: 45.40 % -- Input Database Coverage: 400086741 bp out of 1694434935 bp ( 23.61 % ) Sampling Time: 00:46:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23157415 Comparison Time: 19:45:09 (hh:mm:ss) Elapsed Time, 512951 HSPs Collected Number of families returned by RECON: 45181 Round Time: 21:24:29 (hh:mm:ss) Elapsed Time : 991 families discovered. RepeatScout/RECON discovery complete: 2097 families found Classification Time: 01:06:59 (hh:mm:ss) Elapsed Time Program Time: 26:53:19 (hh:mm:ss) Elapsed Time