RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.syr0C1/RM_212841.FriJan60350352023 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: 1673005835 Database = /dev/shm/rModeler.syr0C1/GCF_009650955.1_bCorMon1.pri - Sequences = 105 - Bases = 1112734094 - N50 = 77816073 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 154691250-165740467 | [ 1 ] 143642033-154691249 | [ ] 132592817-143642033 | [ ] 121543600-132592816 |* [ 2 ] 110494383-121543599 | [ ] 99445167-110494383 | [ ] 88395950-99445166 | [ ] 77346733-88395949 | [ 1 ] 66297517-77346733 |* [ 2 ] 55248300-66297516 | [ 1 ] 44199083-55248299 | [ ] 33149867-44199083 |* [ 2 ] 22100650-33149866 |* [ 2 ] 11051433-22100649 |******* [ 12 ] 2217-11051433 |************************************************** [ 82 ] Storage Throughput = excellent ( 1418.90 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 41004146 bp ( 40006981 non ambiguous ) - Num Contigs Represented = 40 - Sequence extraction : 00:01:46 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:18 (hh:mm:ss) Elapsed Time Round Time: 00:16:57 (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 : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2510 repeats masked totaling 733855 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10202532 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10002640 bp After Masking: 9172164 bp Masked: 8.30 % -- Input Database Coverage: 10202532 bp out of 1112734094 bp ( 0.92 % ) Sampling Time: 00:00:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32896 Comparison Time: 00:06:05 (hh:mm:ss) Elapsed Time, 804 HSPs Collected Number of families returned by RECON: 290 Round Time: 00:07:03 (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 : 00:01:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7197 repeats masked totaling 1919644 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30801534 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 30004261 bp After Masking: 27719153 bp Masked: 7.62 % -- Input Database Coverage: 41004066 bp out of 1112734094 bp ( 3.68 % ) Sampling Time: 00:02:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 296835 Comparison Time: 00:27:08 (hh:mm:ss) Elapsed Time, 7211 HSPs Collected Number of families returned by RECON: 1564 Round Time: 00:30:12 (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 : 00:02:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23251 repeats masked totaling 6626016 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 92214063 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 90018415 bp After Masking: 82289630 bp Masked: 8.59 % -- Input Database Coverage: 133218129 bp out of 1112734094 bp ( 11.97 % ) Sampling Time: 00:06:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2664586 Comparison Time: 02:36:32 (hh:mm:ss) Elapsed Time, 55193 HSPs Collected Number of families returned by RECON: 10052 Round Time: 02:45:49 (hh:mm:ss) Elapsed Time : 88 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 78817 repeats masked totaling 23237049 bp(s). - TE Masking time 00:01:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 276541071 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 270015616 bp After Masking: 243724363 bp Masked: 9.74 % -- Input Database Coverage: 409759200 bp out of 1112734094 bp ( 36.82 % ) Sampling Time: 00:23:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23960503 Comparison Time: 19:06:10 (hh:mm:ss) Elapsed Time, 208587 HSPs Collected Number of families returned by RECON: 71745 Round Time: 20:13:08 (hh:mm:ss) Elapsed Time : 216 families discovered. RepeatScout/RECON discovery complete: 413 families found Classification Time: 00:20:06 (hh:mm:ss) Elapsed Time Program Time: 24:13:15 (hh:mm:ss) Elapsed Time