RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.LRzvwm/RM_21764.MonNov111344492024 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: 1731361486 Database = /dev/shm/rModeler.LRzvwm/GCA_040939525.1_ASM4093952v1 - Sequences = 1782 - Bases = 10901381092 - N50 = 1998597328 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 1871747618-2005443657 | [ 3 ] 1738051580-1871747618 | [ ] 1604355542-1738051580 | [ 1 ] 1470659503-1604355541 | [ ] 1336963465-1470659503 | [ 1 ] 1203267427-1336963465 | [ ] 1069571389-1203267427 | [ ] 935875350-1069571388 | [ 1 ] 802179312-935875350 | [ ] 668483274-802179312 | [ 1 ] 534787236-668483274 | [ ] 401091197-534787235 | [ ] 267395159-401091197 | [ ] 133699121-267395159 | [ ] 3083-133699121 |************************************************** [ 1775 ] Storage Throughput = excellent ( 1192.69 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40015739 bp ( 40011659 non ambiguous ) - Num Contigs Represented = 26 - Sequence extraction : 00:33:50 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:10 (hh:mm:ss) Elapsed Time Round Time: 01:21:54 (hh:mm:ss) Elapsed Time : 736 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:08:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13387 repeats masked totaling 6255482 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000653 bp Num Contigs Represented = 9 Non ambiguous bp: Initial: 9999933 bp After Masking: 3228070 bp Masked: 67.72 % -- Input Database Coverage: 10000653 bp out of 10901381092 bp ( 0.09 % ) Sampling Time: 00:10:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:18 (hh:mm:ss) Elapsed Time, 3939 HSPs Collected Number of families returned by RECON: 880 Round Time: 00:16:33 (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 : 00:25:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 40977 repeats masked totaling 18908657 bp(s). - TE Masking time 00:01:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30015006 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30011646 bp After Masking: 9589389 bp Masked: 68.05 % -- Input Database Coverage: 40015659 bp out of 10901381092 bp ( 0.37 % ) Sampling Time: 00:35:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:21:15 (hh:mm:ss) Elapsed Time, 31045 HSPs Collected Number of families returned by RECON: 2952 Round Time: 00:58:20 (hh:mm:ss) Elapsed Time : 68 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 01:15:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:27:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 127700 repeats masked totaling 57746792 bp(s). - TE Masking time 00:05:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90046238 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 90034478 bp After Masking: 27116368 bp Masked: 69.88 % -- Input Database Coverage: 130061897 bp out of 10901381092 bp ( 1.19 % ) Sampling Time: 01:48:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 01:47:35 (hh:mm:ss) Elapsed Time, 192052 HSPs Collected Number of families returned by RECON: 8912 Round Time: 03:43:39 (hh:mm:ss) Elapsed Time : 289 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 03:46:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:21:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 420003 repeats masked totaling 185365863 bp(s). - TE Masking time 00:18:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270069880 bp Num Contigs Represented = 161 Non ambiguous bp: Initial: 270033064 bp After Masking: 69103354 bp Masked: 74.41 % -- Input Database Coverage: 400131777 bp out of 10901381092 bp ( 3.67 % ) Sampling Time: 05:27:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22926606 Comparison Time: 13:30:18 (hh:mm:ss) Elapsed Time, 581521 HSPs Collected Number of families returned by RECON: 24578 Round Time: 19:35:40 (hh:mm:ss) Elapsed Time : 821 families discovered. RepeatScout/RECON discovery complete: 1916 families found Classification Time: 01:44:39 (hh:mm:ss) Elapsed Time Program Time: 27:40:45 (hh:mm:ss) Elapsed Time