RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.K9zoMR/RM_4880.SunJan140856182024 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: 1705251376 Database = /dev/shm/rModeler.K9zoMR/GCA_032164245.1_rSteOdo2_p1.0 - Sequences = 218 - Bases = 1759411633 - N50 = 114601083 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 286122955-306559226 | [ 1 ] 265686684-286122954 | [ ] 245250414-265686684 | [ ] 224814143-245250413 | [ 1 ] 204377872-224814142 | [ ] 183941602-204377872 | [ ] 163505331-183941601 | [ 1 ] 143069060-163505330 | [ ] 122632790-143069060 | [ ] 102196519-122632789 | [ 4 ] 81760248-102196518 | [ 2 ] 61323978-81760248 | [ 2 ] 40887707-61323977 | [ ] 20451436-40887706 |* [ 5 ] 15166-20451436 |************************************************** [ 202 ] Storage Throughput = excellent ( 1109.59 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40030546 bp ( 40027946 non ambiguous ) - Num Contigs Represented = 42 - Sequence extraction : 00:03:04 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:47 (hh:mm:ss) Elapsed Time Round Time: 00:33:36 (hh:mm:ss) Elapsed Time : 615 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13320 repeats masked totaling 2459429 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040486 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10039686 bp After Masking: 7270015 bp Masked: 27.59 % -- Input Database Coverage: 10040486 bp out of 1759411633 bp ( 0.57 % ) Sampling Time: 00:01:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:08:53 (hh:mm:ss) Elapsed Time, 11487 HSPs Collected Number of families returned by RECON: 1503 Round Time: 00:11:05 (hh:mm:ss) Elapsed Time : 30 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43030 repeats masked totaling 7934572 bp(s). - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30029980 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 30028180 bp After Masking: 21428978 bp Masked: 28.64 % -- Input Database Coverage: 40070466 bp out of 1759411633 bp ( 2.28 % ) Sampling Time: 00:05:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:35:39 (hh:mm:ss) Elapsed Time, 64066 HSPs Collected Number of families returned by RECON: 5207 Round Time: 00:44:21 (hh:mm:ss) Elapsed Time : 146 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 148565 repeats masked totaling 27843169 bp(s). - TE Masking time 00:02:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90012745 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 90008945 bp After Masking: 60307094 bp Masked: 33.00 % -- Input Database Coverage: 130083211 bp out of 1759411633 bp ( 7.39 % ) Sampling Time: 00:14:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 03:34:57 (hh:mm:ss) Elapsed Time, 206438 HSPs Collected Number of families returned by RECON: 14469 Round Time: 04:04:03 (hh:mm:ss) Elapsed Time : 435 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:20:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 522464 repeats masked totaling 96522980 bp(s). - TE Masking time 00:12:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270048382 bp Num Contigs Represented = 104 Non ambiguous bp: Initial: 270033299 bp After Masking: 167804515 bp Masked: 37.86 % -- Input Database Coverage: 400131593 bp out of 1759411633 bp ( 22.74 % ) Sampling Time: 00:50:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22872466 Comparison Time: 26:13:39 (hh:mm:ss) Elapsed Time, 580250 HSPs Collected Number of families returned by RECON: 45566 Round Time: 28:23:57 (hh:mm:ss) Elapsed Time : 1069 families discovered. RepeatScout/RECON discovery complete: 2295 families found Classification Time: 01:27:09 (hh:mm:ss) Elapsed Time Program Time: 35:24:11 (hh:mm:ss) Elapsed Time