RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.PP0Jjj/RM_13503.TueNov120812042024 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: 1731427922 Database = /dev/shm/rModeler.PP0Jjj/GCA_036850995.1_mSacLep1_pri_phased_curated - Sequences = 167 - Bases = 2576497192 - N50 = 372602872 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 366554138-392736510 | [ 3 ] 340371767-366554138 | [ ] 314189395-340371766 | [ ] 288007024-314189395 | [ ] 261824652-288007023 | [ ] 235642281-261824652 | [ ] 209459909-235642280 | [ 2 ] 183277538-209459909 | [ 1 ] 157095166-183277537 | [ ] 130912795-157095166 | [ 1 ] 104730423-130912794 | [ 1 ] 78548052-104730423 |* [ 4 ] 52365680-78548051 | [ 2 ] 26183309-52365680 | [ ] 938-26183309 |************************************************** [ 153 ] Storage Throughput = excellent ( 1063.71 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40250652 bp ( 40018991 non ambiguous ) - Num Contigs Represented = 27 - Sequence extraction : 00:05:21 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:28 (hh:mm:ss) Elapsed Time Round Time: 00:37:41 (hh:mm:ss) Elapsed Time : 292 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12639 repeats masked totaling 3381082 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10126638 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10003505 bp After Masking: 6514483 bp Masked: 34.88 % -- Input Database Coverage: 10126638 bp out of 2576497192 bp ( 0.39 % ) Sampling Time: 00:01:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:05:12 (hh:mm:ss) Elapsed Time, 3772 HSPs Collected Number of families returned by RECON: 711 Round Time: 00:07:31 (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 : 00:04:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 40912 repeats masked totaling 11392593 bp(s). - TE Masking time 00:00:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30124009 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 30015481 bp After Masking: 18225997 bp Masked: 39.28 % -- Input Database Coverage: 40250647 bp out of 2576497192 bp ( 1.56 % ) Sampling Time: 00:05:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:25:42 (hh:mm:ss) Elapsed Time, 21783 HSPs Collected Number of families returned by RECON: 2144 Round Time: 00:32:24 (hh:mm:ss) Elapsed Time : 61 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:11:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 130852 repeats masked totaling 34875603 bp(s). - TE Masking time 00:02:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90550498 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 90016500 bp After Masking: 53885866 bp Masked: 40.14 % -- Input Database Coverage: 130801145 bp out of 2576497192 bp ( 5.08 % ) Sampling Time: 00:17:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2561716 Comparison Time: 02:55:58 (hh:mm:ss) Elapsed Time, 77653 HSPs Collected Number of families returned by RECON: 6980 Round Time: 03:17:01 (hh:mm:ss) Elapsed Time : 167 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:36:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 426571 repeats masked totaling 110557745 bp(s). - TE Masking time 00:08:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271542206 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 270015935 bp After Masking: 155675399 bp Masked: 42.35 % -- Input Database Coverage: 402343351 bp out of 2576497192 bp ( 15.62 % ) Sampling Time: 00:55:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23089410 Comparison Time: 22:55:52 (hh:mm:ss) Elapsed Time, 217684 HSPs Collected Number of families returned by RECON: 30534 Round Time: 24:17:57 (hh:mm:ss) Elapsed Time : 415 families discovered. RepeatScout/RECON discovery complete: 945 families found Classification Time: 00:43:40 (hh:mm:ss) Elapsed Time Program Time: 29:36:14 (hh:mm:ss) Elapsed Time