RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.I4q21X/RM_15163.WedJan111655172023 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: 1673484916 Database = /dev/shm/rModeler.I4q21X/GCA_009769465.1_bTauEry1.pri - Sequences = 140 - Bases = 1252271553 - N50 = 88466996 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 127762775-136888462 | [ 2 ] 118637089-127762775 | [ ] 109511403-118637089 | [ ] 100385717-109511403 | [ 1 ] 91260031-100385717 | [ 1 ] 82134344-91260030 | [ 2 ] 73008658-82134344 | [ 1 ] 63882972-73008658 | [ 1 ] 54757286-63882972 | [ ] 45631600-54757286 | [ ] 36505913-45631599 | [ 2 ] 27380227-36505913 |* [ 3 ] 18254541-27380227 |** [ 6 ] 9128855-18254541 |** [ 6 ] 3169-9128855 |************************************************** [ 115 ] Storage Throughput = excellent ( 1096.67 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40799220 bp ( 40001042 non ambiguous ) - Num Contigs Represented = 48 - Sequence extraction : 00:01:39 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:50 (hh:mm:ss) Elapsed Time Round Time: 00:25:29 (hh:mm:ss) Elapsed Time : 88 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2594 repeats masked totaling 983201 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10244241 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10019851 bp After Masking: 8999048 bp Masked: 10.19 % -- Input Database Coverage: 10244241 bp out of 1252271553 bp ( 0.82 % ) Sampling Time: 00:00:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32896 Comparison Time: 00:07:09 (hh:mm:ss) Elapsed Time, 398 HSPs Collected Number of families returned by RECON: 208 Round Time: 00:08:00 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8509 repeats masked totaling 3285568 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30594899 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 30021111 bp After Masking: 26643457 bp Masked: 11.25 % -- Input Database Coverage: 40839140 bp out of 1252271553 bp ( 3.26 % ) Sampling Time: 00:02:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 292995 Comparison Time: 00:38:33 (hh:mm:ss) Elapsed Time, 5787 HSPs Collected Number of families returned by RECON: 1349 Round Time: 00:41:17 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 25442 repeats masked totaling 9267747 bp(s). - TE Masking time 00:00:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91823912 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 90023140 bp After Masking: 80380659 bp Masked: 10.71 % -- Input Database Coverage: 132663052 bp out of 1252271553 bp ( 10.59 % ) Sampling Time: 00:07:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2653056 Comparison Time: 04:40:17 (hh:mm:ss) Elapsed Time, 39623 HSPs Collected Number of families returned by RECON: 7886 Round Time: 04:49:10 (hh:mm:ss) Elapsed Time : 47 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 85504 repeats masked totaling 29614034 bp(s). - TE Masking time 00:02:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 275646695 bp Num Contigs Represented = 82 Non ambiguous bp: Initial: 270013549 bp After Masking: 239309470 bp Masked: 11.37 % -- Input Database Coverage: 408309747 bp out of 1252271553 bp ( 32.61 % ) Sampling Time: 00:21:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23856778 Comparison Time: 37:45:48 (hh:mm:ss) Elapsed Time, 153575 HSPs Collected Number of families returned by RECON: 52684 Round Time: 38:45:46 (hh:mm:ss) Elapsed Time : 193 families discovered. RepeatScout/RECON discovery complete: 342 families found Classification Time: 00:21:41 (hh:mm:ss) Elapsed Time Program Time: 45:11:23 (hh:mm:ss) Elapsed Time