RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.exy7yd/RM_312836.SunJan81238042023 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: 1673210283 Database = /dev/shm/rModeler.exy7yd/GCA_907165065.1_bCapEur3.1 - Sequences = 121 - Bases = 1177791212 - N50 = 82627501 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 117897965-126318510 |* [ 2 ] 109477420-117897964 | [ ] 101056876-109477420 | [ ] 92636331-101056875 | [ 1 ] 84215787-92636331 | [ ] 75795242-84215786 |* [ 3 ] 67374697-75795241 | [ ] 58954153-67374697 |* [ 2 ] 50533608-58954152 | [ 1 ] 42113064-50533608 |* [ 2 ] 33692519-42113063 | [ 1 ] 25271974-33692518 | [ ] 16851430-25271974 |*** [ 7 ] 8430885-16851429 |** [ 5 ] 10341-8430885 |************************************************** [ 97 ] Storage Throughput = excellent ( 1512.97 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40012658 bp ( 40012058 non ambiguous ) - Num Contigs Represented = 43 - Sequence extraction : 00:01:04 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:56 (hh:mm:ss) Elapsed Time Round Time: 00:22:32 (hh:mm:ss) Elapsed Time : 86 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2282 repeats masked totaling 762087 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10021497 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 10021197 bp After Masking: 9111094 bp Masked: 9.08 % -- Input Database Coverage: 10021497 bp out of 1177791212 bp ( 0.85 % ) Sampling Time: 00:00:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:52 (hh:mm:ss) Elapsed Time, 509 HSPs Collected Number of families returned by RECON: 266 Round Time: 00:06:50 (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 : 00:00:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7109 repeats masked totaling 2449483 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30031161 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 30030861 bp After Masking: 27173171 bp Masked: 9.52 % -- Input Database Coverage: 40052658 bp out of 1177791212 bp ( 3.40 % ) Sampling Time: 00:02:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:28:21 (hh:mm:ss) Elapsed Time, 5296 HSPs Collected Number of families returned by RECON: 1510 Round Time: 00:30:48 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23014 repeats masked totaling 7747428 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90004848 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 90002348 bp After Masking: 80995905 bp Masked: 10.01 % -- Input Database Coverage: 130057506 bp out of 1177791212 bp ( 11.04 % ) Sampling Time: 00:06:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 02:41:25 (hh:mm:ss) Elapsed Time, 53603 HSPs Collected Number of families returned by RECON: 9338 Round Time: 02:50:20 (hh:mm:ss) Elapsed Time : 79 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 80544 repeats masked totaling 26549681 bp(s). - TE Masking time 00:01:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270032505 bp Num Contigs Represented = 68 Non ambiguous bp: Initial: 270026872 bp After Masking: 240257902 bp Masked: 11.02 % -- Input Database Coverage: 400090011 bp out of 1177791212 bp ( 33.97 % ) Sampling Time: 00:17:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22865703 Comparison Time: 18:37:43 (hh:mm:ss) Elapsed Time, 186972 HSPs Collected Number of families returned by RECON: 64551 Round Time: 19:29:52 (hh:mm:ss) Elapsed Time : 233 families discovered. RepeatScout/RECON discovery complete: 409 families found Classification Time: 00:17:04 (hh:mm:ss) Elapsed Time Program Time: 23:37:26 (hh:mm:ss) Elapsed Time