RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.s7qE5U/RM_3651323.ThuMay180839332023 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: 1684424372 Database = /dev/shm/rModeler.s7qE5U/GCF_017976375.1_bCucCan1.pri - Sequences = 150 - Bases = 1180136575 - N50 = 122852502 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 195368946-209323829 | [ 1 ] 181414063-195368945 | [ ] 167459180-181414062 | [ ] 153504297-167459179 | [ 1 ] 139549415-153504297 | [ ] 125594532-139549414 | [ ] 111639649-125594531 | [ 1 ] 97684766-111639648 | [ ] 83729883-97684765 | [ ] 69775001-83729883 | [ 2 ] 55820118-69775000 | [ 1 ] 41865235-55820117 | [ 1 ] 27910352-41865234 |* [ 3 ] 13955469-27910351 |*** [ 9 ] 587-13955469 |************************************************** [ 131 ] Storage Throughput = excellent ( 1179.60 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40143806 bp ( 40015651 non ambiguous ) - Num Contigs Represented = 46 - Sequence extraction : 00:01:47 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:12 (hh:mm:ss) Elapsed Time Round Time: 00:18:26 (hh:mm:ss) Elapsed Time : 85 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3050 repeats masked totaling 879971 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004494 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10003794 bp After Masking: 8939035 bp Masked: 10.64 % -- Input Database Coverage: 10004494 bp out of 1180136575 bp ( 0.85 % ) Sampling Time: 00:01:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:07:32 (hh:mm:ss) Elapsed Time, 597 HSPs Collected Number of families returned by RECON: 252 Round Time: 00:08:40 (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 : 00:01:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10039 repeats masked totaling 2833869 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30139232 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 30011777 bp After Masking: 26724195 bp Masked: 10.95 % -- Input Database Coverage: 40143726 bp out of 1180136575 bp ( 3.40 % ) Sampling Time: 00:03:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:35:57 (hh:mm:ss) Elapsed Time, 5911 HSPs Collected Number of families returned by RECON: 1254 Round Time: 00:39:17 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 29687 repeats masked totaling 8321998 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90424816 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 90027193 bp After Masking: 80047957 bp Masked: 11.08 % -- Input Database Coverage: 130568542 bp out of 1180136575 bp ( 11.06 % ) Sampling Time: 00:09:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2566245 Comparison Time: 03:44:19 (hh:mm:ss) Elapsed Time, 49378 HSPs Collected Number of families returned by RECON: 7970 Round Time: 03:55:56 (hh:mm:ss) Elapsed Time : 71 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 101692 repeats masked totaling 28652017 bp(s). - TE Masking time 00:02:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271093294 bp Num Contigs Represented = 89 Non ambiguous bp: Initial: 270030195 bp After Masking: 236952581 bp Masked: 12.25 % -- Input Database Coverage: 401661836 bp out of 1180136575 bp ( 34.04 % ) Sampling Time: 00:26:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23130201 Comparison Time: 26:03:34 (hh:mm:ss) Elapsed Time, 185622 HSPs Collected Number of families returned by RECON: 49612 Round Time: 26:55:13 (hh:mm:ss) Elapsed Time : 215 families discovered. RepeatScout/RECON discovery complete: 381 families found Classification Time: 00:20:33 (hh:mm:ss) Elapsed Time Program Time: 32:18:05 (hh:mm:ss) Elapsed Time