RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.vzvQmI/RM_25005.FriJan61304232023 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: 1673039062 Database = /dev/shm/rModeler.vzvQmI/GCF_009819885.2_bCatUst1.pri.v2 - Sequences = 160 - Bases = 1131616530 - N50 = 76913702 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 154722696-165774257 | [ 1 ] 143671135-154722695 | [ ] 132619575-143671135 | [ ] 121568014-132619574 | [ 1 ] 110516454-121568014 | [ 1 ] 99464893-110516453 | [ ] 88413332-99464892 | [ ] 77361772-88413332 | [ ] 66310211-77361771 |* [ 3 ] 55258651-66310211 | [ 1 ] 44207090-55258650 | [ ] 33155529-44207089 |* [ 3 ] 22103969-33155529 | [ 2 ] 11052408-22103968 |**** [ 11 ] 848-11052408 |************************************************* [ 137 ] Storage Throughput = excellent ( 1115.53 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40739504 bp ( 40010344 non ambiguous ) - Num Contigs Represented = 49 - Sequence extraction : 00:01:40 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:28 (hh:mm:ss) Elapsed Time Round Time: 00:27:07 (hh:mm:ss) Elapsed Time : 141 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2810 repeats masked totaling 751174 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10158828 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 10038612 bp After Masking: 8993452 bp Masked: 10.41 % -- Input Database Coverage: 10158828 bp out of 1131616530 bp ( 0.90 % ) Sampling Time: 00:01:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:07:12 (hh:mm:ss) Elapsed Time, 926 HSPs Collected Number of families returned by RECON: 295 Round Time: 00:08:39 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9362 repeats masked totaling 2418030 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30620613 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 30011669 bp After Masking: 26579937 bp Masked: 11.43 % -- Input Database Coverage: 40779441 bp out of 1131616530 bp ( 3.60 % ) Sampling Time: 00:03:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 294528 Comparison Time: 00:40:25 (hh:mm:ss) Elapsed Time, 8035 HSPs Collected Number of families returned by RECON: 1860 Round Time: 00:45:12 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 28077 repeats masked totaling 7247553 bp(s). - TE Masking time 00:00:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90788132 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 90036807 bp After Masking: 79774325 bp Masked: 11.40 % -- Input Database Coverage: 131567573 bp out of 1131616530 bp ( 11.63 % ) Sampling Time: 00:10:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2595781 Comparison Time: 04:51:30 (hh:mm:ss) Elapsed Time, 60275 HSPs Collected Number of families returned by RECON: 11392 Round Time: 05:06:59 (hh:mm:ss) Elapsed Time : 107 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 91906 repeats masked totaling 23794675 bp(s). - TE Masking time 00:04:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 273747692 bp Num Contigs Represented = 98 Non ambiguous bp: Initial: 270003105 bp After Masking: 237760984 bp Masked: 11.94 % -- Input Database Coverage: 405315265 bp out of 1131616530 bp ( 35.82 % ) Sampling Time: 00:34:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23567545 Comparison Time: 39:29:16 (hh:mm:ss) Elapsed Time, 225227 HSPs Collected Number of families returned by RECON: 73731 Round Time: 41:29:56 (hh:mm:ss) Elapsed Time : 300 families discovered. RepeatScout/RECON discovery complete: 562 families found Classification Time: 01:08:12 (hh:mm:ss) Elapsed Time Program Time: 49:06:05 (hh:mm:ss) Elapsed Time