RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.jC7EHt/RM_22641.FriDec81859232023 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: 1702090762 Database = /dev/shm/rModeler.jC7EHt/GCA_951394435.1_mSteCoe1.1 - Sequences = 638 - Bases = 2691423227 - N50 = 111291038 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 177490100-190167893 | [ 2 ] 164812307-177490099 | [ 1 ] 152134514-164812306 | [ ] 139456721-152134513 | [ 2 ] 126778928-139456720 | [ 1 ] 114101135-126778927 | [ 2 ] 101423342-114101134 | [ 4 ] 88745550-101423342 | [ 3 ] 76067757-88745549 | [ 4 ] 63389964-76067756 | [ ] 50712171-63389963 | [ 2 ] 38034378-50712170 | [ ] 25356585-38034377 | [ 1 ] 12678792-25356584 | [ ] 1000-12678792 |************************************************** [ 616 ] Storage Throughput = excellent ( 1118.80 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40033182 bp ( 40029382 non ambiguous ) - Num Contigs Represented = 114 - Sequence extraction : 00:02:18 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:27:49 (hh:mm:ss) Elapsed Time Round Time: 00:41:25 (hh:mm:ss) Elapsed Time : 177 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9680 repeats masked totaling 2682656 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004302 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 10003902 bp After Masking: 6992960 bp Masked: 30.10 % -- Input Database Coverage: 10004302 bp out of 2691423227 bp ( 0.37 % ) Sampling Time: 00:01:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:36 (hh:mm:ss) Elapsed Time, 329935 HSPs Collected Number of families returned by RECON: 802 Round Time: 00:18:12 (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 : 00:01:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34720 repeats masked totaling 11097004 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30028879 bp Num Contigs Represented = 96 Non ambiguous bp: Initial: 30025479 bp After Masking: 18321446 bp Masked: 38.98 % -- Input Database Coverage: 40033181 bp out of 2691423227 bp ( 1.49 % ) Sampling Time: 00:03:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:26:43 (hh:mm:ss) Elapsed Time, 24187 HSPs Collected Number of families returned by RECON: 2222 Round Time: 00:31:34 (hh:mm:ss) Elapsed Time : 65 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 110929 repeats masked totaling 35100903 bp(s). - TE Masking time 00:01:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90035531 bp Num Contigs Represented = 220 Non ambiguous bp: Initial: 90028331 bp After Masking: 51699040 bp Masked: 42.57 % -- Input Database Coverage: 130068712 bp out of 2691423227 bp ( 4.83 % ) Sampling Time: 00:13:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 02:46:47 (hh:mm:ss) Elapsed Time, 87544 HSPs Collected Number of families returned by RECON: 7544 Round Time: 03:03:48 (hh:mm:ss) Elapsed Time : 159 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 366823 repeats masked totaling 112130339 bp(s). - TE Masking time 00:05:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270028485 bp Num Contigs Represented = 337 Non ambiguous bp: Initial: 270008885 bp After Masking: 150268754 bp Masked: 44.35 % -- Input Database Coverage: 400097197 bp out of 2691423227 bp ( 14.87 % ) Sampling Time: 00:38:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23069028 Comparison Time: 21:08:16 (hh:mm:ss) Elapsed Time, 431221 HSPs Collected Number of families returned by RECON: 29913 Round Time: 22:43:08 (hh:mm:ss) Elapsed Time : 355 families discovered. RepeatScout/RECON discovery complete: 776 families found Classification Time: 00:36:17 (hh:mm:ss) Elapsed Time Program Time: 27:54:24 (hh:mm:ss) Elapsed Time