RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.yKDQiO/RM_1255924.FriFeb142046172025 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: 1739594775 Database = /dev/shm/rModeler.yKDQiO/GCA_905221615.1_Stri_CCMP2592 - Sequences = 6245 - Bases = 1103301044 - N50 = 652178 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 3742499-4009728 | [ 3 ] 3475271-3742499 | [ ] 3208042-3475270 | [ 1 ] 2940814-3208042 | [ 3 ] 2673586-2940814 | [ 4 ] 2406357-2673585 | [ 2 ] 2139129-2406357 | [ 9 ] 1871900-2139128 | [ 22 ] 1604672-1871900 | [ 30 ] 1337444-1604672 | [ 49 ] 1070215-1337443 | [ 82 ] 802987-1070215 |* [ 148 ] 535758-802986 |** [ 274 ] 268530-535758 |***** [ 579 ] 1302-268530 |************************************************** [ 5039 ] Storage Throughput = excellent ( 1807.24 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40033022 bp ( 40027222 non ambiguous ) - Num Contigs Represented = 874 - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:05:52 (hh:mm:ss) Elapsed Time Round Time: 00:13:31 (hh:mm:ss) Elapsed Time : 424 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13129 repeats masked totaling 2104317 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10007147 bp Num Contigs Represented = 257 Non ambiguous bp: Initial: 10005347 bp After Masking: 7280896 bp Masked: 27.23 % -- Input Database Coverage: 10007147 bp out of 1103301044 bp ( 0.91 % ) Sampling Time: 00:00:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 38226 Comparison Time: 00:02:53 (hh:mm:ss) Elapsed Time, 3867 HSPs Collected Number of families returned by RECON: 768 Round Time: 00:04:07 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 41446 repeats masked totaling 6757373 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30025795 bp Num Contigs Represented = 692 Non ambiguous bp: Initial: 30021795 bp After Masking: 21350925 bp Masked: 28.88 % -- Input Database Coverage: 40032942 bp out of 1103301044 bp ( 3.63 % ) Sampling Time: 00:01:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 361675 Comparison Time: 00:11:26 (hh:mm:ss) Elapsed Time, 19907 HSPs Collected Number of families returned by RECON: 3253 Round Time: 00:14:15 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 126142 repeats masked totaling 19921187 bp(s). - TE Masking time 00:01:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90024035 bp Num Contigs Represented = 1532 Non ambiguous bp: Initial: 90009835 bp After Masking: 64403420 bp Masked: 28.45 % -- Input Database Coverage: 130056977 bp out of 1103301044 bp ( 11.79 % ) Sampling Time: 00:05:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3138765 Comparison Time: 01:03:13 (hh:mm:ss) Elapsed Time, 212138 HSPs Collected Number of families returned by RECON: 13503 Round Time: 01:16:53 (hh:mm:ss) Elapsed Time : 207 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 404150 repeats masked totaling 74380557 bp(s). - TE Masking time 00:05:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270063621 bp Num Contigs Represented = 2917 Non ambiguous bp: Initial: 270022621 bp After Masking: 178653125 bp Masked: 33.84 % -- Input Database Coverage: 400120598 bp out of 1103301044 bp ( 36.27 % ) Sampling Time: 00:19:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 28959855 Comparison Time: 06:53:21 (hh:mm:ss) Elapsed Time, 1094291 HSPs Collected Number of families returned by RECON: 50392 Round Time: 07:46:24 (hh:mm:ss) Elapsed Time : 807 families discovered. RepeatScout/RECON discovery complete: 1460 families found Classification Time: 01:41:51 (hh:mm:ss) Elapsed Time Program Time: 11:17:01 (hh:mm:ss) Elapsed Time