RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.XR2tRx/RM_3557.MonMay150911252023 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: 1684167085 Database = /dev/shm/rModeler.XR2tRx/GCF_024139225.1_mSunEtr1.pri.cur - Sequences = 147 - Bases = 2471666657 - N50 = 131976403 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 194361924-208244741 | [ 1 ] 180479108-194361924 | [ ] 166596292-180479108 |* [ 3 ] 152713476-166596292 | [ 1 ] 138830660-152713476 | [ ] 124947844-138830660 |* [ 3 ] 111065028-124947844 |* [ 3 ] 97182211-111065027 |* [ 4 ] 83299395-97182211 | [ 2 ] 69416579-83299395 | [ 1 ] 55533763-69416579 | [ 1 ] 41650947-55533763 | [ 2 ] 27768131-41650947 | [ ] 13885315-27768131 | [ ] 2499-13885315 |************************************************** [ 126 ] Storage Throughput = fair ( 525.27 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40201534 bp ( 40004874 non ambiguous ) - Num Contigs Represented = 27 - Sequence extraction : 00:02:45 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:19 (hh:mm:ss) Elapsed Time Round Time: 00:39:37 (hh:mm:ss) Elapsed Time : 323 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:32 (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... 19134 repeats masked totaling 4192036 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040410 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10016440 bp After Masking: 5579833 bp Masked: 44.29 % -- Input Database Coverage: 10040410 bp out of 2471666657 bp ( 0.41 % ) Sampling Time: 00:03:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:07:59 (hh:mm:ss) Elapsed Time, 1924 HSPs Collected Number of families returned by RECON: 443 Round Time: 00:11:55 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:04:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 56897 repeats masked totaling 12185017 bp(s). - TE Masking time 00:01:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30201124 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 30028434 bp After Masking: 17089503 bp Masked: 43.09 % -- Input Database Coverage: 40241534 bp out of 2471666657 bp ( 1.63 % ) Sampling Time: 00:10:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:38:22 (hh:mm:ss) Elapsed Time, 18921 HSPs Collected Number of families returned by RECON: 1757 Round Time: 00:51:00 (hh:mm:ss) Elapsed Time : 44 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:09:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 183733 repeats masked totaling 37963994 bp(s). - TE Masking time 00:04:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90569780 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 90029704 bp After Masking: 49771652 bp Masked: 44.72 % -- Input Database Coverage: 130811314 bp out of 2471666657 bp ( 5.29 % ) Sampling Time: 00:20:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2570778 Comparison Time: 04:12:40 (hh:mm:ss) Elapsed Time, 58434 HSPs Collected Number of families returned by RECON: 5612 Round Time: 04:36:17 (hh:mm:ss) Elapsed Time : 144 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:40:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 575768 repeats masked totaling 117210464 bp(s). - TE Masking time 00:13:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270897477 bp Num Contigs Represented = 57 Non ambiguous bp: Initial: 270035205 bp After Masking: 146100451 bp Masked: 45.90 % -- Input Database Coverage: 401708791 bp out of 2471666657 bp ( 16.25 % ) Sampling Time: 01:12:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22974031 Comparison Time: 32:38:28 (hh:mm:ss) Elapsed Time, 196415 HSPs Collected Number of families returned by RECON: 24355 Round Time: 34:09:46 (hh:mm:ss) Elapsed Time : 324 families discovered. RepeatScout/RECON discovery complete: 839 families found Classification Time: 01:21:04 (hh:mm:ss) Elapsed Time Program Time: 41:49:39 (hh:mm:ss) Elapsed Time