RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.8ygqkO/RM_47273.SatJun291618042024 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: 1719703082 Database = /dev/shm/rModeler.8ygqkO/GCF_905237065.1_Ssal_v3.1 - Sequences = 4011 - Bases = 2756584103 - N50 = 96486271 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 162865514-174498729 | [ 1 ] 151232300-162865514 | [ 1 ] 139599086-151232300 | [ ] 127965871-139599085 | [ ] 116332657-127965871 | [ 1 ] 104699443-116332657 | [ 4 ] 93066229-104699443 | [ 6 ] 81433014-93066228 | [ 5 ] 69799800-81433014 | [ ] 58166586-69799800 | [ 3 ] 46533372-58166586 | [ 4 ] 34900157-46533371 | [ 3 ] 23266943-34900157 | [ 1 ] 11633729-23266943 | [ ] 515-11633729 |************************************************** [ 3982 ] Storage Throughput = excellent ( 1309.25 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40002997 bp ( 40002697 non ambiguous ) - Num Contigs Represented = 148 - Sequence extraction : 00:01:49 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:49 (hh:mm:ss) Elapsed Time Round Time: 00:22:37 (hh:mm:ss) Elapsed Time : 816 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12686 repeats masked totaling 3698606 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10029365 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 10029265 bp After Masking: 3912301 bp Masked: 60.99 % -- Input Database Coverage: 10029365 bp out of 2756584103 bp ( 0.36 % ) Sampling Time: 00:06:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33411 Comparison Time: 00:05:19 (hh:mm:ss) Elapsed Time, 4453 HSPs Collected Number of families returned by RECON: 970 Round Time: 00:11:46 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 38491 repeats masked totaling 11229342 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30013629 bp Num Contigs Represented = 124 Non ambiguous bp: Initial: 30013429 bp After Masking: 11196553 bp Masked: 62.69 % -- Input Database Coverage: 40042994 bp out of 2756584103 bp ( 1.45 % ) Sampling Time: 00:22:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 297606 Comparison Time: 00:18:26 (hh:mm:ss) Elapsed Time, 32198 HSPs Collected Number of families returned by RECON: 3269 Round Time: 00:41:21 (hh:mm:ss) Elapsed Time : 90 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:53:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 124370 repeats masked totaling 35314290 bp(s). - TE Masking time 00:01:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90035056 bp Num Contigs Represented = 276 Non ambiguous bp: Initial: 90034356 bp After Masking: 34109430 bp Masked: 62.12 % -- Input Database Coverage: 130078050 bp out of 2756584103 bp ( 4.72 % ) Sampling Time: 00:58:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2669205 Comparison Time: 01:30:48 (hh:mm:ss) Elapsed Time, 247190 HSPs Collected Number of families returned by RECON: 9640 Round Time: 02:34:20 (hh:mm:ss) Elapsed Time : 498 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 02:36:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 422379 repeats masked totaling 117367999 bp(s). - TE Masking time 00:05:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270018542 bp Num Contigs Represented = 769 Non ambiguous bp: Initial: 270016742 bp After Masking: 88066556 bp Masked: 67.38 % -- Input Database Coverage: 400096592 bp out of 2756584103 bp ( 14.51 % ) Sampling Time: 02:54:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24252130 Comparison Time: 09:44:00 (hh:mm:ss) Elapsed Time, 618413 HSPs Collected Number of families returned by RECON: 30399 Round Time: 13:00:23 (hh:mm:ss) Elapsed Time : 941 families discovered. RepeatScout/RECON discovery complete: 2350 families found Classification Time: 01:00:44 (hh:mm:ss) Elapsed Time Program Time: 17:51:11 (hh:mm:ss) Elapsed Time