RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.uvI56O/RM_1719707.TueMar261700032024 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: 1711497602 Database = /dev/shm/rModeler.uvI56O/GCA_963662255.1_bCinCin1.1 - Sequences = 278 - Bases = 1170855695 - N50 = 74413991 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 142206966-152364536 | [ 1 ] 132049397-142206966 | [ ] 121891828-132049397 | [ ] 111734259-121891828 | [ 2 ] 101576690-111734259 | [ ] 91419121-101576690 | [ ] 81261552-91419121 | [ 1 ] 71103983-81261552 | [ 2 ] 60946414-71103983 | [ 1 ] 50788845-60946414 | [ ] 40631276-50788845 | [ ] 30473707-40631276 | [ 2 ] 20316138-30473707 |* [ 7 ] 10158569-20316138 |* [ 7 ] 1000-10158569 |************************************************** [ 255 ] Storage Throughput = excellent ( 1381.89 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40019005 bp ( 40014605 non ambiguous ) - Num Contigs Represented = 81 - Sequence extraction : 00:01:23 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:49 (hh:mm:ss) Elapsed Time Round Time: 00:24:10 (hh:mm:ss) Elapsed Time : 98 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2298 repeats masked totaling 640238 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10018437 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 10017437 bp After Masking: 8718062 bp Masked: 12.97 % -- Input Database Coverage: 10018437 bp out of 1170855695 bp ( 0.86 % ) Sampling Time: 00:01:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:36 (hh:mm:ss) Elapsed Time, 1446 HSPs Collected Number of families returned by RECON: 248 Round Time: 00:08:32 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6755 repeats masked totaling 1789765 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30040506 bp Num Contigs Represented = 76 Non ambiguous bp: Initial: 30037106 bp After Masking: 25476519 bp Masked: 15.18 % -- Input Database Coverage: 40058943 bp out of 1170855695 bp ( 3.42 % ) Sampling Time: 00:04:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:32:32 (hh:mm:ss) Elapsed Time, 8780 HSPs Collected Number of families returned by RECON: 1466 Round Time: 00:37:53 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21576 repeats masked totaling 5642986 bp(s). - TE Masking time 00:00:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90041325 bp Num Contigs Represented = 126 Non ambiguous bp: Initial: 90030110 bp After Masking: 76374943 bp Masked: 15.17 % -- Input Database Coverage: 130100268 bp out of 1170855695 bp ( 11.11 % ) Sampling Time: 00:15:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 03:52:17 (hh:mm:ss) Elapsed Time, 188797 HSPs Collected Number of families returned by RECON: 9106 Round Time: 04:15:53 (hh:mm:ss) Elapsed Time : 77 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:39:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 72720 repeats masked totaling 20081519 bp(s). - TE Masking time 00:03:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270062069 bp Num Contigs Represented = 172 Non ambiguous bp: Initial: 270030554 bp After Masking: 228589826 bp Masked: 15.35 % -- Input Database Coverage: 400162337 bp out of 1170855695 bp ( 34.18 % ) Sampling Time: 00:53:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23007936 Comparison Time: 29:09:00 (hh:mm:ss) Elapsed Time, 636729 HSPs Collected Number of families returned by RECON: 63423 Round Time: 30:56:34 (hh:mm:ss) Elapsed Time : 222 families discovered. RepeatScout/RECON discovery complete: 407 families found Classification Time: 00:41:07 (hh:mm:ss) Elapsed Time Program Time: 37:04:09 (hh:mm:ss) Elapsed Time