RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.1rRCLJ/RM_710345.SunJul70408062024 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: 1720350486 Database = /dev/shm/rModeler.1rRCLJ/GCF_033978685.1_RoL_Nlum_1.0 - Sequences = 630 - Bases = 3157240560 - N50 = 49364683 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 73931020-79211643 | [ 4 ] 68650397-73931019 | [ 1 ] 63369775-68650397 | [ 4 ] 58089152-63369774 | [ 6 ] 52808529-58089151 | [ 8 ] 47527907-52808529 | [ 4 ] 42247284-47527906 | [ 11 ] 36966661-42247283 | [ 6 ] 31686039-36966661 | [ 4 ] 26405416-31686038 | [ 8 ] 21124793-26405415 | [ 9 ] 15844171-21124793 | [ 3 ] 10563548-15844170 | [ 1 ] 5282925-10563547 | [ 1 ] 2303-5282925 |************************************************** [ 560 ] Storage Throughput = excellent ( 1235.53 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40014363 bp ( 40014303 non ambiguous ) - Num Contigs Represented = 102 - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:21 (hh:mm:ss) Elapsed Time Round Time: 00:37:24 (hh:mm:ss) Elapsed Time : 1341 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22496 repeats masked totaling 5399614 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027008 bp Num Contigs Represented = 75 Non ambiguous bp: Initial: 10027008 bp After Masking: 3302349 bp Masked: 67.07 % -- Input Database Coverage: 10027008 bp out of 3157240560 bp ( 0.32 % ) Sampling Time: 00:02:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:04:29 (hh:mm:ss) Elapsed Time, 8734 HSPs Collected Number of families returned by RECON: 1083 Round Time: 00:06:51 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 70825 repeats masked totaling 16541064 bp(s). - TE Masking time 00:01:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30027275 bp Num Contigs Represented = 95 Non ambiguous bp: Initial: 30027215 bp After Masking: 9985240 bp Masked: 66.75 % -- Input Database Coverage: 40054283 bp out of 3157240560 bp ( 1.27 % ) Sampling Time: 00:05:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:19:26 (hh:mm:ss) Elapsed Time, 47193 HSPs Collected Number of families returned by RECON: 3419 Round Time: 00:26:29 (hh:mm:ss) Elapsed Time : 120 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 218538 repeats masked totaling 50031592 bp(s). - TE Masking time 00:03:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90016513 bp Num Contigs Represented = 120 Non ambiguous bp: Initial: 90016413 bp After Masking: 28413845 bp Masked: 68.43 % -- Input Database Coverage: 130070796 bp out of 3157240560 bp ( 4.12 % ) Sampling Time: 00:18:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 01:42:07 (hh:mm:ss) Elapsed Time, 251795 HSPs Collected Number of families returned by RECON: 8907 Round Time: 02:06:38 (hh:mm:ss) Elapsed Time : 556 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:36:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 728292 repeats masked totaling 164607880 bp(s). - TE Masking time 00:14:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270014122 bp Num Contigs Represented = 176 Non ambiguous bp: Initial: 270013702 bp After Masking: 73333803 bp Masked: 72.84 % -- Input Database Coverage: 400084918 bp out of 3157240560 bp ( 12.67 % ) Sampling Time: 00:55:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22913065 Comparison Time: 10:13:50 (hh:mm:ss) Elapsed Time, 627631 HSPs Collected Number of families returned by RECON: 23082 Round Time: 11:34:27 (hh:mm:ss) Elapsed Time : 1130 families discovered. RepeatScout/RECON discovery complete: 3159 families found Classification Time: 01:47:43 (hh:mm:ss) Elapsed Time Program Time: 16:39:32 (hh:mm:ss) Elapsed Time