RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.oGT4sb/RM_12952.ThuJul111049162024 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: 1720720151 Database = /dev/shm/rModeler.oGT4sb/GCF_002775205.1_X_maculatus-5.0-male - Sequences = 102 - Bases = 704321165 - N50 = 31544005 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 32940880-35293739 |** [ 4 ] 30588022-32940880 |**** [ 7 ] 28235164-30588022 |** [ 4 ] 25882305-28235163 |** [ 4 ] 23529447-25882305 |* [ 3 ] 21176589-23529447 | [ ] 18823730-21176588 | [ 1 ] 16470872-18823730 | [ ] 14118014-16470872 | [ 1 ] 11765155-14118013 | [ ] 9412297-11765155 | [ ] 7059439-9412297 | [ ] 4706580-7059438 | [ ] 2353722-4706580 | [ ] 864-2353722 |************************************************** [ 78 ] Storage Throughput = excellent ( 1044.55 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40114612 bp ( 40005614 non ambiguous ) - Num Contigs Represented = 28 - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:16 (hh:mm:ss) Elapsed Time Round Time: 00:28:59 (hh:mm:ss) Elapsed Time : 428 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9512 repeats masked totaling 1326889 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10063104 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10027912 bp After Masking: 8495028 bp Masked: 15.29 % -- Input Database Coverage: 10063104 bp out of 704321165 bp ( 1.43 % ) Sampling Time: 00:01:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:13:26 (hh:mm:ss) Elapsed Time, 11800 HSPs Collected Number of families returned by RECON: 1612 Round Time: 00:15:04 (hh:mm:ss) Elapsed Time : 26 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30506 repeats masked totaling 4664005 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30091508 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 30017702 bp After Masking: 24795558 bp Masked: 17.40 % -- Input Database Coverage: 40154612 bp out of 704321165 bp ( 5.70 % ) Sampling Time: 00:02:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:38:30 (hh:mm:ss) Elapsed Time, 42709 HSPs Collected Number of families returned by RECON: 4938 Round Time: 00:42:42 (hh:mm:ss) Elapsed Time : 117 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 108132 repeats masked totaling 16953223 bp(s). - TE Masking time 00:01:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90492826 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 90006065 bp After Masking: 71530516 bp Masked: 20.53 % -- Input Database Coverage: 130647438 bp out of 704321165 bp ( 18.55 % ) Sampling Time: 00:07:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2570778 Comparison Time: 04:27:24 (hh:mm:ss) Elapsed Time, 237169 HSPs Collected Number of families returned by RECON: 15951 Round Time: 04:47:01 (hh:mm:ss) Elapsed Time : 422 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 390100 repeats masked totaling 64269473 bp(s). - TE Masking time 00:11:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271479532 bp Num Contigs Represented = 69 Non ambiguous bp: Initial: 270013391 bp After Masking: 201393916 bp Masked: 25.41 % -- Input Database Coverage: 402126970 bp out of 704321165 bp ( 57.09 % ) Sampling Time: 00:26:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23164221 Comparison Time: 33:56:41 (hh:mm:ss) Elapsed Time, 624963 HSPs Collected Number of families returned by RECON: 58251 Round Time: 35:55:17 (hh:mm:ss) Elapsed Time : 941 families discovered. RepeatScout/RECON discovery complete: 1934 families found Classification Time: 01:39:43 (hh:mm:ss) Elapsed Time Program Time: 43:48:46 (hh:mm:ss) Elapsed Time