RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.bnTrVf/RM_2759887.SunMar170835592024 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: 1710689758 Database = /dev/shm/rModeler.bnTrVf/GCA_036172335.1_bHelExo1.hap2 - Sequences = 200 - Bases = 969853240 - N50 = 150173037 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 183955633-197094454 | [ 1 ] 170816812-183955632 | [ ] 157677992-170816812 | [ ] 144539171-157677991 | [ 1 ] 131400351-144539171 | [ ] 118261530-131400350 | [ ] 105122709-118261529 | [ 1 ] 91983889-105122709 | [ ] 78845068-91983888 | [ ] 65706248-78845068 | [ ] 52567427-65706247 | [ ] 39428606-52567426 | [ 2 ] 26289786-39428606 | [ 3 ] 13150965-26289785 |*** [ 11 ] 12145-13150965 |************************************************** [ 181 ] Storage Throughput = excellent ( 1239.45 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40020681 bp ( 40017881 non ambiguous ) - Num Contigs Represented = 58 - Sequence extraction : 00:01:51 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:27 (hh:mm:ss) Elapsed Time Round Time: 00:21:18 (hh:mm:ss) Elapsed Time : 97 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:33 (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... 2762 repeats masked totaling 640917 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10006890 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10005290 bp After Masking: 9068280 bp Masked: 9.37 % -- Input Database Coverage: 10006890 bp out of 969853240 bp ( 1.03 % ) Sampling Time: 00:01:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:07:14 (hh:mm:ss) Elapsed Time, 594 HSPs Collected Number of families returned by RECON: 309 Round Time: 00:08:32 (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 : 00:01:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8309 repeats masked totaling 2062380 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30013789 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 30012589 bp After Masking: 26798117 bp Masked: 10.71 % -- Input Database Coverage: 40020679 bp out of 969853240 bp ( 4.13 % ) Sampling Time: 00:03:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:38:20 (hh:mm:ss) Elapsed Time, 4658 HSPs Collected Number of families returned by RECON: 1785 Round Time: 00:42:31 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23301 repeats masked totaling 5466799 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90012466 bp Num Contigs Represented = 78 Non ambiguous bp: Initial: 90005966 bp After Masking: 81950256 bp Masked: 8.95 % -- Input Database Coverage: 130033145 bp out of 969853240 bp ( 13.41 % ) Sampling Time: 00:10:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2566245 Comparison Time: 04:29:57 (hh:mm:ss) Elapsed Time, 41886 HSPs Collected Number of families returned by RECON: 12458 Round Time: 04:43:31 (hh:mm:ss) Elapsed Time : 52 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 80124 repeats masked totaling 18847370 bp(s). - TE Masking time 00:02:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270031751 bp Num Contigs Represented = 132 Non ambiguous bp: Initial: 270010451 bp After Masking: 243747283 bp Masked: 9.73 % -- Input Database Coverage: 400064896 bp out of 969853240 bp ( 41.25 % ) Sampling Time: 00:34:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22940151 Comparison Time: 36:57:16 (hh:mm:ss) Elapsed Time, 234031 HSPs Collected Number of families returned by RECON: 85357 Round Time: 38:37:43 (hh:mm:ss) Elapsed Time : 200 families discovered. RepeatScout/RECON discovery complete: 353 families found Classification Time: 00:21:22 (hh:mm:ss) Elapsed Time Program Time: 44:54:57 (hh:mm:ss) Elapsed Time