RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.izIAM1/RM_27452.WedNov131604462024 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: 1731542685 Database = /scratch/tmp/rModeler.izIAM1/GCF_036850995.1_mSacLep1_pri_phased_curated - Sequences = 168 - Bases = 2576513769 - 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 |************************************************** [ 154 ] Storage Throughput = fair ( 593.87 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40330462 bp ( 40034322 non ambiguous ) - Num Contigs Represented = 28 - Sequence extraction : 00:05:21 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:39 (hh:mm:ss) Elapsed Time Round Time: 00:35:41 (hh:mm:ss) Elapsed Time : 281 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12746 repeats masked totaling 3428776 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10082650 bp Num Contigs Represented = 17 Non ambiguous bp: Initial: 10001957 bp After Masking: 6427331 bp Masked: 35.74 % -- Input Database Coverage: 10082650 bp out of 2576513769 bp ( 0.39 % ) Sampling Time: 00:02:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:05 (hh:mm:ss) Elapsed Time, 6551 HSPs Collected Number of families returned by RECON: 795 Round Time: 00:07:50 (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 : 00:03:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44573 repeats masked totaling 11236467 bp(s). - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30247732 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30032285 bp After Masking: 18367840 bp Masked: 38.84 % -- Input Database Coverage: 40330382 bp out of 2576513769 bp ( 1.57 % ) Sampling Time: 00:05:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:25:47 (hh:mm:ss) Elapsed Time, 21168 HSPs Collected Number of families returned by RECON: 1976 Round Time: 00:32:36 (hh:mm:ss) Elapsed Time : 51 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:11:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 135881 repeats masked totaling 35040768 bp(s). - TE Masking time 00:02:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90610236 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 90038110 bp After Masking: 53792943 bp Masked: 40.26 % -- Input Database Coverage: 130940618 bp out of 2576513769 bp ( 5.08 % ) Sampling Time: 00:17:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2570778 Comparison Time: 02:56:57 (hh:mm:ss) Elapsed Time, 86917 HSPs Collected Number of families returned by RECON: 6824 Round Time: 03:18:56 (hh:mm:ss) Elapsed Time : 192 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:35:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 445573 repeats masked totaling 113462514 bp(s). - TE Masking time 00:08:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 273030988 bp Num Contigs Represented = 75 Non ambiguous bp: Initial: 270009887 bp After Masking: 152703805 bp Masked: 43.45 % -- Input Database Coverage: 403971606 bp out of 2576513769 bp ( 15.68 % ) Sampling Time: 00:55:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23368866 Comparison Time: 22:37:31 (hh:mm:ss) Elapsed Time, 201813 HSPs Collected Number of families returned by RECON: 27120 Round Time: 23:59:27 (hh:mm:ss) Elapsed Time : 356 families discovered. RepeatScout/RECON discovery complete: 893 families found Classification Time: 00:41:09 (hh:mm:ss) Elapsed Time Program Time: 29:15:39 (hh:mm:ss) Elapsed Time