RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.CRmW6W/RM_1839050.FriDec61643382024 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: 1733532217 Database = /scratch/tmp/rModeler.CRmW6W/GCA_964194205.1_mTalEur1.hap2.1 - Sequences = 356 - Bases = 2056471431 - N50 = 138729880 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 148570263-159182354 | [ 3 ] 137958173-148570263 | [ 3 ] 127346083-137958173 | [ 1 ] 116733992-127346082 | [ 3 ] 106121902-116733992 | [ ] 95509812-106121902 | [ 4 ] 84897722-95509812 | [ 2 ] 74285631-84897721 | [ ] 63673541-74285631 | [ ] 53061451-63673541 | [ ] 42449361-53061451 | [ 1 ] 31837270-42449360 | [ ] 21225180-31837270 | [ ] 10613090-21225180 | [ ] 1000-10613090 |************************************************** [ 339 ] Storage Throughput = excellent ( 1550.56 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40022413 bp ( 40018813 non ambiguous ) - Num Contigs Represented = 30 - Sequence extraction : 00:01:19 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:34 (hh:mm:ss) Elapsed Time Round Time: 00:15:34 (hh:mm:ss) Elapsed Time : 155 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9130 repeats masked totaling 2352026 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10035594 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 10034594 bp After Masking: 7629565 bp Masked: 23.97 % -- Input Database Coverage: 10035594 bp out of 2056471431 bp ( 0.49 % ) Sampling Time: 00:00:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:15 (hh:mm:ss) Elapsed Time, 5332 HSPs Collected Number of families returned by RECON: 779 Round Time: 00:03:59 (hh:mm:ss) Elapsed Time : 22 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 29012 repeats masked totaling 7204960 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30026819 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 30024219 bp After Masking: 22528584 bp Masked: 24.97 % -- Input Database Coverage: 40062413 bp out of 2056471431 bp ( 1.95 % ) Sampling Time: 00:01:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:14:18 (hh:mm:ss) Elapsed Time, 17199 HSPs Collected Number of families returned by RECON: 2252 Round Time: 00:16:26 (hh:mm:ss) Elapsed Time : 47 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 93769 repeats masked totaling 23768720 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90040447 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 90030647 bp After Masking: 65335912 bp Masked: 27.43 % -- Input Database Coverage: 130102860 bp out of 2056471431 bp ( 6.33 % ) Sampling Time: 00:05:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 01:21:48 (hh:mm:ss) Elapsed Time, 91194 HSPs Collected Number of families returned by RECON: 8476 Round Time: 01:29:09 (hh:mm:ss) Elapsed Time : 156 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 318571 repeats masked totaling 79582358 bp(s). - TE Masking time 00:01:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270052623 bp Num Contigs Represented = 103 Non ambiguous bp: Initial: 270026320 bp After Masking: 187403430 bp Masked: 30.60 % -- Input Database Coverage: 400155483 bp out of 2056471431 bp ( 19.46 % ) Sampling Time: 00:16:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22933378 Comparison Time: 09:28:19 (hh:mm:ss) Elapsed Time, 275509 HSPs Collected Number of families returned by RECON: 38317 Round Time: 10:01:23 (hh:mm:ss) Elapsed Time : 457 families discovered. RepeatScout/RECON discovery complete: 837 families found Classification Time: 00:20:14 (hh:mm:ss) Elapsed Time Program Time: 12:26:45 (hh:mm:ss) Elapsed Time