RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.bmP1w7/RM_4155314.WedMar200032462024 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: 1710919966 Database = /dev/shm/rModeler.bmP1w7/GCA_036321565.1_mCamDro1.hap2 - Sequences = 173 - Bases = 2086495379 - N50 = 76389953 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 114090414-122238078 |* [ 3 ] 105942751-114090414 | [ ] 97795088-105942751 | [ 1 ] 89647425-97795088 | [ 2 ] 81499762-89647425 | [ 2 ] 73352098-81499761 | [ 2 ] 65204435-73352098 |* [ 3 ] 57056772-65204435 | [ 2 ] 48909109-57056772 | [ 1 ] 40761446-48909109 |* [ 3 ] 32613782-40761445 |* [ 3 ] 24466119-32613782 |** [ 7 ] 16318456-24466119 |** [ 7 ] 8170793-16318456 | [ 1 ] 23130-8170793 |************************************************* [ 136 ] Storage Throughput = good ( 984.66 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40023299 bp ( 40022099 non ambiguous ) - Num Contigs Represented = 73 - Sequence extraction : 00:01:26 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:09 (hh:mm:ss) Elapsed Time Round Time: 00:23:31 (hh:mm:ss) Elapsed Time : 175 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 00:00:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6863 repeats masked totaling 1374904 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10024547 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 10024347 bp After Masking: 7698625 bp Masked: 23.20 % -- Input Database Coverage: 10024547 bp out of 2086495379 bp ( 0.48 % ) Sampling Time: 00:01:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:03 (hh:mm:ss) Elapsed Time, 5599 HSPs Collected Number of families returned by RECON: 886 Round Time: 00:07:29 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 24192 repeats masked totaling 4865511 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30038672 bp Num Contigs Represented = 67 Non ambiguous bp: Initial: 30037672 bp After Masking: 22714494 bp Masked: 24.38 % -- Input Database Coverage: 40063219 bp out of 2086495379 bp ( 1.92 % ) Sampling Time: 00:03:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:28:51 (hh:mm:ss) Elapsed Time, 29528 HSPs Collected Number of families returned by RECON: 2832 Round Time: 00:33:09 (hh:mm:ss) Elapsed Time : 72 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 84731 repeats masked totaling 17737555 bp(s). - TE Masking time 00:00:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90035823 bp Num Contigs Represented = 89 Non ambiguous bp: Initial: 90033223 bp After Masking: 64880246 bp Masked: 27.94 % -- Input Database Coverage: 130099042 bp out of 2086495379 bp ( 6.24 % ) Sampling Time: 00:09:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 03:03:33 (hh:mm:ss) Elapsed Time, 81334 HSPs Collected Number of families returned by RECON: 9597 Round Time: 03:16:53 (hh:mm:ss) Elapsed Time : 169 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 290684 repeats masked totaling 62040723 bp(s). - TE Masking time 00:04:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270031564 bp Num Contigs Represented = 125 Non ambiguous bp: Initial: 270026564 bp After Masking: 185599104 bp Masked: 31.27 % -- Input Database Coverage: 400130606 bp out of 2086495379 bp ( 19.18 % ) Sampling Time: 00:28:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22858941 Comparison Time: 21:25:33 (hh:mm:ss) Elapsed Time, 664853 HSPs Collected Number of families returned by RECON: 41699 Round Time: 22:54:48 (hh:mm:ss) Elapsed Time : 303 families discovered. RepeatScout/RECON discovery complete: 736 families found Classification Time: 00:39:04 (hh:mm:ss) Elapsed Time Program Time: 27:54:54 (hh:mm:ss) Elapsed Time