RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.t43GwZ/RM_21374.MonMay81021332023 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: 1683566490 Database = /dev/shm/rModeler.t43GwZ/GCA_027474245.1_bSphHub1.pri - Sequences = 136 - Bases = 1358357718 - N50 = 136016534 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 216107153-231542106 | [ 1 ] 200672200-216107152 | [ ] 185237248-200672200 | [ ] 169802295-185237247 | [ 1 ] 154367342-169802294 | [ ] 138932390-154367342 | [ ] 123497437-138932389 | [ 1 ] 108062484-123497436 | [ ] 92627532-108062484 | [ ] 77192579-92627531 |* [ 4 ] 61757626-77192578 | [ 1 ] 46322674-61757626 | [ ] 30887721-46322673 | [ 1 ] 15452768-30887720 |*** [ 9 ] 17816-15452768 |************************************************** [ 118 ] Storage Throughput = excellent ( 1095.72 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40014152 bp ( 40009412 non ambiguous ) - Num Contigs Represented = 47 - Sequence extraction : 00:02:19 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:55 (hh:mm:ss) Elapsed Time Round Time: 00:34:06 (hh:mm:ss) Elapsed Time : 38 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1150 repeats masked totaling 753347 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10009786 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 10009322 bp After Masking: 8660029 bp Masked: 13.48 % -- Input Database Coverage: 10009786 bp out of 1358357718 bp ( 0.74 % ) Sampling Time: 00:01:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:10:57 (hh:mm:ss) Elapsed Time, 605 HSPs Collected Number of families returned by RECON: 237 Round Time: 00:12:33 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4023 repeats masked totaling 2583658 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30004286 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 30000010 bp After Masking: 25936815 bp Masked: 13.54 % -- Input Database Coverage: 40014072 bp out of 1358357718 bp ( 2.95 % ) Sampling Time: 00:05:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:49:17 (hh:mm:ss) Elapsed Time, 6269 HSPs Collected Number of families returned by RECON: 1376 Round Time: 00:55:21 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14713 repeats masked totaling 7761844 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90096667 bp Num Contigs Represented = 57 Non ambiguous bp: Initial: 90026696 bp After Masking: 77936048 bp Masked: 13.43 % -- Input Database Coverage: 130110739 bp out of 1358357718 bp ( 9.58 % ) Sampling Time: 00:10:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 04:57:59 (hh:mm:ss) Elapsed Time, 73697 HSPs Collected Number of families returned by RECON: 8174 Round Time: 05:16:46 (hh:mm:ss) Elapsed Time : 69 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 57914 repeats masked totaling 26637928 bp(s). - TE Masking time 00:02:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270312390 bp Num Contigs Represented = 83 Non ambiguous bp: Initial: 270011954 bp After Masking: 230199252 bp Masked: 14.74 % -- Input Database Coverage: 400423129 bp out of 1358357718 bp ( 29.48 % ) Sampling Time: 00:33:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22926606 Comparison Time: 34:59:49 (hh:mm:ss) Elapsed Time, 189234 HSPs Collected Number of families returned by RECON: 50401 Round Time: 36:21:55 (hh:mm:ss) Elapsed Time : 209 families discovered. RepeatScout/RECON discovery complete: 335 families found Classification Time: 00:30:33 (hh:mm:ss) Elapsed Time Program Time: 43:51:14 (hh:mm:ss) Elapsed Time