RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.AtWVkI/RM_55274.MonJan160513082023 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: 1673874786 Database = /dev/shm/rModeler.AtWVkI/GCA_004115265.2_mRhiFer1_v1.p - Sequences = 135 - Bases = 2075785400 - N50 = 89119429 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 116605608-124933378 | [ 1 ] 108277839-116605608 | [ 1 ] 99950070-108277839 |* [ 4 ] 91622300-99950069 |* [ 3 ] 83294531-91622300 |* [ 3 ] 74966762-83294531 | [ ] 66638992-74966761 |* [ 4 ] 58311223-66638992 | [ 2 ] 49983454-58311223 |* [ 4 ] 41655684-49983453 | [ 2 ] 33327915-41655684 | [ 1 ] 25000146-33327915 | [ 2 ] 16672376-25000145 | [ 2 ] 8344607-16672376 | [ 1 ] 16838-8344607 |************************************************** [ 105 ] Storage Throughput = excellent ( 1728.91 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40228401 bp ( 40034857 non ambiguous ) - Num Contigs Represented = 38 - Sequence extraction : 00:01:07 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:11:10 (hh:mm:ss) Elapsed Time Round Time: 00:17:23 (hh:mm:ss) Elapsed Time : 181 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 00:00:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7482 repeats masked totaling 2067949 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10080800 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10007717 bp After Masking: 7873927 bp Masked: 21.32 % -- Input Database Coverage: 10080800 bp out of 2075785400 bp ( 0.49 % ) Sampling Time: 00:00:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:49 (hh:mm:ss) Elapsed Time, 8538 HSPs Collected Number of families returned by RECON: 1095 Round Time: 00:06:59 (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 : 00:01:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 27922 repeats masked totaling 7249013 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30147521 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 30027060 bp After Masking: 22507749 bp Masked: 25.04 % -- Input Database Coverage: 40228321 bp out of 2075785400 bp ( 1.94 % ) Sampling Time: 00:02:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:25:14 (hh:mm:ss) Elapsed Time, 27251 HSPs Collected Number of families returned by RECON: 2502 Round Time: 00:28:06 (hh:mm:ss) Elapsed Time : 74 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 92350 repeats masked totaling 23251053 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90295756 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 90004823 bp After Masking: 66071032 bp Masked: 26.59 % -- Input Database Coverage: 130524077 bp out of 2075785400 bp ( 6.29 % ) Sampling Time: 00:05:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 02:11:45 (hh:mm:ss) Elapsed Time, 73385 HSPs Collected Number of families returned by RECON: 9360 Round Time: 02:19:32 (hh:mm:ss) Elapsed Time : 158 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 315222 repeats masked totaling 78357197 bp(s). - TE Masking time 00:02:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270897569 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 270031262 bp After Masking: 189618009 bp Masked: 29.78 % -- Input Database Coverage: 401421646 bp out of 2075785400 bp ( 19.34 % ) Sampling Time: 00:18:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22953700 Comparison Time: 15:59:37 (hh:mm:ss) Elapsed Time, 199390 HSPs Collected Number of families returned by RECON: 39403 Round Time: 16:36:44 (hh:mm:ss) Elapsed Time : 381 families discovered. RepeatScout/RECON discovery complete: 820 families found Classification Time: 00:22:21 (hh:mm:ss) Elapsed Time Program Time: 20:11:05 (hh:mm:ss) Elapsed Time