RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.id0dmD/RM_2186984.ThuJun270609122024 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: 1719493751 Database = /dev/shm/rModeler.id0dmD/GCF_036321535.1_mCamDro1.pat - Sequences = 171 - Bases = 2306603094 - N50 = 79033285 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 115066378-123284173 |* [ 3 ] 106848584-115066378 | [ 1 ] 98630789-106848583 | [ ] 90412995-98630789 |* [ 3 ] 82195200-90412994 | [ 2 ] 73977406-82195200 | [ 2 ] 65759611-73977405 |* [ 4 ] 57541817-65759611 | [ 2 ] 49324022-57541816 | [ ] 41106228-49324022 |* [ 3 ] 32888433-41106227 |* [ 5 ] 24670639-32888433 |** [ 7 ] 16452844-24670638 |* [ 5 ] 8235050-16452844 | [ 2 ] 17256-8235050 |************************************************** [ 132 ] Storage Throughput = excellent ( 1361.36 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40002959 bp ( 40002159 non ambiguous ) - Num Contigs Represented = 74 - Sequence extraction : 00:01:21 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:45 (hh:mm:ss) Elapsed Time Round Time: 00:23:28 (hh:mm:ss) Elapsed Time : 183 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6887 repeats masked totaling 1816466 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001716 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 10001116 bp After Masking: 7183481 bp Masked: 28.17 % -- Input Database Coverage: 10001716 bp out of 2306603094 bp ( 0.43 % ) Sampling Time: 00:01:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:18 (hh:mm:ss) Elapsed Time, 5517 HSPs Collected Number of families returned by RECON: 768 Round Time: 00:07:08 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22631 repeats masked totaling 5553878 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001163 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 30000963 bp After Masking: 21471381 bp Masked: 28.43 % -- Input Database Coverage: 40002879 bp out of 2306603094 bp ( 1.73 % ) Sampling Time: 00:03:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:25:05 (hh:mm:ss) Elapsed Time, 23154 HSPs Collected Number of families returned by RECON: 2299 Round Time: 00:28:59 (hh:mm:ss) Elapsed Time : 61 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 79054 repeats masked totaling 19612405 bp(s). - TE Masking time 00:01:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90010320 bp Num Contigs Represented = 103 Non ambiguous bp: Initial: 90008520 bp After Masking: 60921155 bp Masked: 32.32 % -- Input Database Coverage: 130013199 bp out of 2306603094 bp ( 5.64 % ) Sampling Time: 00:09:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 02:41:13 (hh:mm:ss) Elapsed Time, 84978 HSPs Collected Number of families returned by RECON: 8302 Round Time: 02:53:41 (hh:mm:ss) Elapsed Time : 143 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 263105 repeats masked totaling 64892859 bp(s). - TE Masking time 00:04:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270014246 bp Num Contigs Represented = 138 Non ambiguous bp: Initial: 270009846 bp After Masking: 176379018 bp Masked: 34.68 % -- Input Database Coverage: 400027445 bp out of 2306603094 bp ( 17.34 % ) Sampling Time: 00:32:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22811635 Comparison Time: 20:38:51 (hh:mm:ss) Elapsed Time, 320743 HSPs Collected Number of families returned by RECON: 38063 Round Time: 22:02:07 (hh:mm:ss) Elapsed Time : 321 families discovered. RepeatScout/RECON discovery complete: 723 families found Classification Time: 00:42:34 (hh:mm:ss) Elapsed Time Program Time: 26:37:57 (hh:mm:ss) Elapsed Time