RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.8ezlqB/RM_8605.SunJan141357222024 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: 1705269440 Database = /dev/shm/rModeler.8ezlqB/GCA_033296515.1_rMacSuw1.hap1 - Sequences = 366 - Bases = 2132261265 - N50 = 145236352 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 322688317-345736556 | [ 1 ] 299640078-322688316 | [ ] 276591840-299640078 | [ ] 253543601-276591839 | [ 1 ] 230495363-253543601 | [ ] 207447124-230495362 | [ ] 184398886-207447124 | [ 1 ] 161350647-184398885 | [ ] 138302409-161350647 | [ 2 ] 115254170-138302408 | [ 2 ] 92205932-115254170 | [ 3 ] 69157693-92205931 | [ 1 ] 46109455-69157693 | [ ] 23061216-46109454 | [ 6 ] 12978-23061216 |************************************************** [ 349 ] Storage Throughput = excellent ( 1097.53 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40035995 bp ( 40034595 non ambiguous ) - Num Contigs Represented = 40 - Sequence extraction : 00:03:22 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:23 (hh:mm:ss) Elapsed Time Round Time: 00:31:19 (hh:mm:ss) Elapsed Time : 573 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13490 repeats masked totaling 2796332 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10011249 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10010649 bp After Masking: 7083019 bp Masked: 29.25 % -- Input Database Coverage: 10011249 bp out of 2132261265 bp ( 0.47 % ) Sampling Time: 00:01:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:06:59 (hh:mm:ss) Elapsed Time, 14225 HSPs Collected Number of families returned by RECON: 1705 Round Time: 00:09:04 (hh:mm:ss) Elapsed Time : 28 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44666 repeats masked totaling 9387187 bp(s). - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30024713 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 30023913 bp After Masking: 20189423 bp Masked: 32.76 % -- Input Database Coverage: 40035962 bp out of 2132261265 bp ( 1.88 % ) Sampling Time: 00:05:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:38:21 (hh:mm:ss) Elapsed Time, 67979 HSPs Collected Number of families returned by RECON: 5140 Round Time: 00:46:03 (hh:mm:ss) Elapsed Time : 143 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 152328 repeats masked totaling 31781806 bp(s). - TE Masking time 00:02:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90010934 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 90007934 bp After Masking: 57184983 bp Masked: 36.47 % -- Input Database Coverage: 130046896 bp out of 2132261265 bp ( 6.10 % ) Sampling Time: 00:14:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 03:39:02 (hh:mm:ss) Elapsed Time, 238995 HSPs Collected Number of families returned by RECON: 14204 Round Time: 04:09:06 (hh:mm:ss) Elapsed Time : 467 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:23:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 532273 repeats masked totaling 111114967 bp(s). - TE Masking time 00:12:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270025987 bp Num Contigs Represented = 89 Non ambiguous bp: Initial: 270019587 bp After Masking: 155943650 bp Masked: 42.25 % -- Input Database Coverage: 400072883 bp out of 2132261265 bp ( 18.76 % ) Sampling Time: 00:47:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22919835 Comparison Time: 24:18:40 (hh:mm:ss) Elapsed Time, 1632254 HSPs Collected Number of families returned by RECON: 45364 Round Time: 26:38:56 (hh:mm:ss) Elapsed Time : 1006 families discovered. RepeatScout/RECON discovery complete: 2217 families found Classification Time: 01:30:50 (hh:mm:ss) Elapsed Time Program Time: 33:45:18 (hh:mm:ss) Elapsed Time