RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Rqiylv/RM_111105.SunJan81824202023 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: 1673231060 Database = /dev/shm/rModeler.Rqiylv/GCA_901699155.2_bStrTur1.2 - Sequences = 311 - Bases = 1178816852 - N50 = 126219232 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 207307789-222115097 | [ 1 ] 192500482-207307789 | [ ] 177693174-192500481 | [ ] 162885867-177693174 | [ 1 ] 148078560-162885867 | [ ] 133271252-148078559 | [ ] 118463945-133271252 | [ 1 ] 103656637-118463944 | [ ] 88849330-103656637 | [ ] 74042023-88849330 | [ 2 ] 59234715-74042022 | [ 1 ] 44427408-59234715 | [ ] 29620100-44427407 | [ 3 ] 14812793-29620100 |* [ 9 ] 5486-14812793 |************************************************** [ 293 ] Storage Throughput = excellent ( 1100.82 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40189608 bp ( 40013983 non ambiguous ) - Num Contigs Represented = 53 - Sequence extraction : 00:02:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:03 (hh:mm:ss) Elapsed Time Round Time: 00:26:33 (hh:mm:ss) Elapsed Time : 89 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2159 repeats masked totaling 739588 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10028813 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10027435 bp After Masking: 9200201 bp Masked: 8.25 % -- Input Database Coverage: 10028813 bp out of 1178816852 bp ( 0.85 % ) Sampling Time: 00:01:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:07:18 (hh:mm:ss) Elapsed Time, 728 HSPs Collected Number of families returned by RECON: 265 Round Time: 00:08:42 (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 : 00:02:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6178 repeats masked totaling 2131568 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30200795 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 30026548 bp After Masking: 27689500 bp Masked: 7.78 % -- Input Database Coverage: 40229608 bp out of 1178816852 bp ( 3.41 % ) Sampling Time: 00:03:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:38:48 (hh:mm:ss) Elapsed Time, 4313 HSPs Collected Number of families returned by RECON: 1343 Round Time: 00:42:33 (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 : 00:06:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20406 repeats masked totaling 6879935 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90512093 bp Num Contigs Represented = 74 Non ambiguous bp: Initial: 90028471 bp After Masking: 82547412 bp Masked: 8.31 % -- Input Database Coverage: 130741701 bp out of 1178816852 bp ( 11.09 % ) Sampling Time: 00:10:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2582128 Comparison Time: 04:05:25 (hh:mm:ss) Elapsed Time, 52240 HSPs Collected Number of families returned by RECON: 8536 Round Time: 04:19:08 (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 : 00:15:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 75186 repeats masked totaling 24686531 bp(s). - TE Masking time 00:02:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271220840 bp Num Contigs Represented = 156 Non ambiguous bp: Initial: 270016333 bp After Masking: 243460964 bp Masked: 9.83 % -- Input Database Coverage: 401962541 bp out of 1178816852 bp ( 34.10 % ) Sampling Time: 00:27:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23211891 Comparison Time: 33:51:37 (hh:mm:ss) Elapsed Time, 207954 HSPs Collected Number of families returned by RECON: 54174 Round Time: 34:58:26 (hh:mm:ss) Elapsed Time : 218 families discovered. RepeatScout/RECON discovery complete: 394 families found Classification Time: 00:48:09 (hh:mm:ss) Elapsed Time Program Time: 41:23:31 (hh:mm:ss) Elapsed Time