RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.9DzchX/RM_24235.FriJul191058162024 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: 1721411891 Database = /dev/shm/rModeler.9DzchX/GCF_014851395.1_ASM1485139v1 - Sequences = 4753 - Bases = 963613914 - N50 = 36690384 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 62897411-67390012 | [ 1 ] 58404810-62897410 | [ ] 53912209-58404809 | [ 1 ] 49419608-53912208 | [ ] 44927008-49419608 | [ ] 40434407-44927007 | [ 2 ] 35941806-40434406 | [ 8 ] 31449205-35941805 | [ 8 ] 26956604-31449204 | [ 1 ] 22464004-26956604 | [ 2 ] 17971403-22464003 | [ ] 13478802-17971402 | [ ] 8986201-13478801 | [ ] 4493600-8986200 | [ ] 1000-4493600 |************************************************** [ 4730 ] Storage Throughput = good ( 725.49 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40074441 bp ( 40014900 non ambiguous ) - Num Contigs Represented = 245 - Sequence extraction : 00:00:47 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:54 (hh:mm:ss) Elapsed Time Round Time: 00:37:03 (hh:mm:ss) Elapsed Time : 1061 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14034 repeats masked totaling 2353326 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10033078 bp Num Contigs Represented = 87 Non ambiguous bp: Initial: 10018228 bp After Masking: 7385942 bp Masked: 26.27 % -- Input Database Coverage: 10033078 bp out of 963613914 bp ( 1.04 % ) Sampling Time: 00:01:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 40470 Comparison Time: 00:23:47 (hh:mm:ss) Elapsed Time, 8956 HSPs Collected Number of families returned by RECON: 1829 Round Time: 00:26:12 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 41423 repeats masked totaling 6880895 bp(s). - TE Masking time 00:00:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30081363 bp Num Contigs Represented = 181 Non ambiguous bp: Initial: 30036672 bp After Masking: 22599741 bp Masked: 24.76 % -- Input Database Coverage: 40114441 bp out of 963613914 bp ( 4.16 % ) Sampling Time: 00:03:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 354903 Comparison Time: 01:24:01 (hh:mm:ss) Elapsed Time, 60287 HSPs Collected Number of families returned by RECON: 6277 Round Time: 01:31:59 (hh:mm:ss) Elapsed Time : 163 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 137095 repeats masked totaling 22872120 bp(s). - TE Masking time 00:02:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90175506 bp Num Contigs Represented = 468 Non ambiguous bp: Initial: 90031274 bp After Masking: 64973952 bp Masked: 27.83 % -- Input Database Coverage: 130289947 bp out of 963613914 bp ( 13.52 % ) Sampling Time: 00:10:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3059101 Comparison Time: 06:58:22 (hh:mm:ss) Elapsed Time, 361524 HSPs Collected Number of families returned by RECON: 19681 Round Time: 07:37:56 (hh:mm:ss) Elapsed Time : 688 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 500373 repeats masked totaling 87910768 bp(s). - TE Masking time 00:16:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270431678 bp Num Contigs Represented = 1459 Non ambiguous bp: Initial: 270008862 bp After Masking: 175892012 bp Masked: 34.86 % -- Input Database Coverage: 400721625 bp out of 963613914 bp ( 41.59 % ) Sampling Time: 00:38:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 28121250 Comparison Time: 30:16:01 (hh:mm:ss) Elapsed Time, 1161234 HSPs Collected Number of families returned by RECON: 60532 Round Time: 33:02:48 (hh:mm:ss) Elapsed Time : 1404 families discovered. RepeatScout/RECON discovery complete: 3330 families found Classification Time: 02:27:59 (hh:mm:ss) Elapsed Time Program Time: 45:43:58 (hh:mm:ss) Elapsed Time