RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.EKmlDF/RM_21778.SunJan81449362023 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: 1673218175 Database = /dev/shm/rModeler.EKmlDF/GCA_922990625.1_mMelMel3.1_maternal_haplotype_uncurated - Sequences = 726 - Bases = 2692729365 - N50 = 119073601 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 196790415-210845944 | [ 1 ] 182734887-196790415 | [ 1 ] 168679359-182734887 | [ ] 154623831-168679359 | [ 2 ] 140568303-154623831 | [ 1 ] 126512775-140568303 | [ ] 112457247-126512775 | [ 5 ] 98401718-112457246 | [ ] 84346190-98401718 | [ 2 ] 70290662-84346190 | [ 4 ] 56235134-70290662 | [ 2 ] 42179606-56235134 | [ 4 ] 28124078-42179606 | [ 1 ] 14068550-28124078 | [ 7 ] 13022-14068550 |************************************************** [ 696 ] Storage Throughput = excellent ( 1164.46 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40038782 bp ( 40038782 non ambiguous ) - Num Contigs Represented = 98 - Sequence extraction : 00:02:04 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:20 (hh:mm:ss) Elapsed Time Round Time: 00:34:22 (hh:mm:ss) Elapsed Time : 179 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11283 repeats masked totaling 2995769 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10035992 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 10035992 bp After Masking: 6961594 bp Masked: 30.63 % -- Input Database Coverage: 10035992 bp out of 2692729365 bp ( 0.37 % ) Sampling Time: 00:01:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:49 (hh:mm:ss) Elapsed Time, 8798 HSPs Collected Number of families returned by RECON: 749 Round Time: 00:08:17 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36306 repeats masked totaling 9785342 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30002779 bp Num Contigs Represented = 79 Non ambiguous bp: Initial: 30002779 bp After Masking: 19948407 bp Masked: 33.51 % -- Input Database Coverage: 40038771 bp out of 2692729365 bp ( 1.49 % ) Sampling Time: 00:03:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:31:34 (hh:mm:ss) Elapsed Time, 21936 HSPs Collected Number of families returned by RECON: 2214 Round Time: 00:35:46 (hh:mm:ss) Elapsed Time : 48 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 114775 repeats masked totaling 30265445 bp(s). - TE Masking time 00:01:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90040020 bp Num Contigs Represented = 151 Non ambiguous bp: Initial: 90039520 bp After Masking: 59085536 bp Masked: 34.38 % -- Input Database Coverage: 130078791 bp out of 2692729365 bp ( 4.83 % ) Sampling Time: 00:09:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 03:55:52 (hh:mm:ss) Elapsed Time, 336545 HSPs Collected Number of families returned by RECON: 8481 Round Time: 04:09:30 (hh:mm:ss) Elapsed Time : 155 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 395892 repeats masked totaling 97600330 bp(s). - TE Masking time 00:06:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270028358 bp Num Contigs Represented = 282 Non ambiguous bp: Initial: 270026358 bp After Masking: 170423378 bp Masked: 36.89 % -- Input Database Coverage: 400107149 bp out of 2692729365 bp ( 14.86 % ) Sampling Time: 00:29:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23035078 Comparison Time: 28:06:33 (hh:mm:ss) Elapsed Time, 2237526 HSPs Collected Number of families returned by RECON: 34516 Round Time: 29:30:21 (hh:mm:ss) Elapsed Time : 360 families discovered. RepeatScout/RECON discovery complete: 762 families found Classification Time: 00:42:39 (hh:mm:ss) Elapsed Time Program Time: 35:40:55 (hh:mm:ss) Elapsed Time