RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.JrMHGn/RM_2651908.MonMar250845162024 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: 1711381515 Database = /dev/shm/rModeler.JrMHGn/GCA_036426135.1_mEquCab1.pat - Sequences = 602 - Bases = 2596737506 - N50 = 94532046 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 179474783-192293490 | [ 1 ] 166656076-179474782 | [ ] 153837369-166656075 | [ ] 141018662-153837368 | [ ] 128199956-141018662 | [ 2 ] 115381249-128199955 | [ 2 ] 102562542-115381248 | [ 1 ] 89743835-102562541 | [ 6 ] 76925128-89743834 | [ 4 ] 64106422-76925128 | [ 2 ] 51287715-64106421 | [ 5 ] 38469008-51287714 | [ 6 ] 25650301-38469007 | [ 3 ] 12831594-25650300 | [ 1 ] 12888-12831594 |************************************************** [ 569 ] Storage Throughput = excellent ( 1414.30 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036174 bp ( 40035574 non ambiguous ) - Num Contigs Represented = 50 - Sequence extraction : 00:01:43 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:28 (hh:mm:ss) Elapsed Time Round Time: 00:24:44 (hh:mm:ss) Elapsed Time : 209 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 00:00:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8831 repeats masked totaling 2110461 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004262 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 10003662 bp After Masking: 7326755 bp Masked: 26.76 % -- Input Database Coverage: 10004262 bp out of 2596737506 bp ( 0.39 % ) Sampling Time: 00:01:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:07:39 (hh:mm:ss) Elapsed Time, 17982 HSPs Collected Number of families returned by RECON: 929 Round Time: 00:09:17 (hh:mm:ss) Elapsed Time : 19 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31338 repeats masked totaling 7640875 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30031910 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 30031910 bp After Masking: 21244860 bp Masked: 29.26 % -- Input Database Coverage: 40036172 bp out of 2596737506 bp ( 1.54 % ) Sampling Time: 00:02:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:37:07 (hh:mm:ss) Elapsed Time, 98148 HSPs Collected Number of families returned by RECON: 2701 Round Time: 00:40:59 (hh:mm:ss) Elapsed Time : 69 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 102280 repeats masked totaling 24742207 bp(s). - TE Masking time 00:00:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90019301 bp Num Contigs Represented = 86 Non ambiguous bp: Initial: 90017901 bp After Masking: 61466699 bp Masked: 31.72 % -- Input Database Coverage: 130055473 bp out of 2596737506 bp ( 5.01 % ) Sampling Time: 00:09:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2563980 Comparison Time: 03:24:54 (hh:mm:ss) Elapsed Time, 3173060 HSPs Collected Number of families returned by RECON: 9912 Round Time: 03:39:44 (hh:mm:ss) Elapsed Time : 186 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 351001 repeats masked totaling 83865064 bp(s). - TE Masking time 00:04:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270009283 bp Num Contigs Represented = 174 Non ambiguous bp: Initial: 270007683 bp After Masking: 174123045 bp Masked: 35.51 % -- Input Database Coverage: 400064756 bp out of 2596737506 bp ( 15.41 % ) Sampling Time: 00:28:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22953700 Comparison Time: 23:23:48 (hh:mm:ss) Elapsed Time, 29866627 HSPs Collected Number of families returned by RECON: 38510 Round Time: 24:31:32 (hh:mm:ss) Elapsed Time : 376 families discovered. RepeatScout/RECON discovery complete: 859 families found Classification Time: 00:42:34 (hh:mm:ss) Elapsed Time Program Time: 30:08:50 (hh:mm:ss) Elapsed Time