RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ZcoSoI/RM_9077.MonNov271342382023 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: 1701121357 Database = /dev/shm/rModeler.ZcoSoI/GCF_030435755.1_mOchPri1.hap1 - Sequences = 5864 - Bases = 2555444530 - N50 = 78426614 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 160986133-172484232 | [ 2 ] 149488034-160986132 | [ ] 137989935-149488033 | [ ] 126491837-137989935 | [ ] 114993738-126491836 | [ 1 ] 103495639-114993737 | [ 3 ] 91997540-103495638 | [ ] 80499442-91997540 | [ 4 ] 69001343-80499441 | [ 4 ] 57503244-69001342 | [ 3 ] 46005145-57503243 | [ 3 ] 34507047-46005145 | [ 5 ] 23008948-34507046 | [ 6 ] 11510849-23008947 | [ 3 ] 12751-11510849 |************************************************** [ 5830 ] Storage Throughput = excellent ( 1140.13 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40034656 bp ( 40033456 non ambiguous ) - Num Contigs Represented = 199 - Sequence extraction : 00:01:37 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:44 (hh:mm:ss) Elapsed Time Round Time: 00:48:29 (hh:mm:ss) Elapsed Time : 182 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11375 repeats masked totaling 2639928 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10028737 bp Num Contigs Represented = 73 Non ambiguous bp: Initial: 10028537 bp After Masking: 5881819 bp Masked: 41.35 % -- Input Database Coverage: 10028737 bp out of 2555444530 bp ( 0.39 % ) Sampling Time: 00:01:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33411 Comparison Time: 00:05:34 (hh:mm:ss) Elapsed Time, 2523 HSPs Collected Number of families returned by RECON: 393 Round Time: 00:07:12 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34183 repeats masked totaling 8069677 bp(s). - TE Masking time 00:00:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30005917 bp Num Contigs Represented = 162 Non ambiguous bp: Initial: 30004917 bp After Masking: 17500916 bp Masked: 41.67 % -- Input Database Coverage: 40034654 bp out of 2555444530 bp ( 1.57 % ) Sampling Time: 00:03:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 303031 Comparison Time: 00:26:07 (hh:mm:ss) Elapsed Time, 16519 HSPs Collected Number of families returned by RECON: 1553 Round Time: 00:31:37 (hh:mm:ss) Elapsed Time : 29 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 111405 repeats masked totaling 25488721 bp(s). - TE Masking time 00:01:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90039575 bp Num Contigs Represented = 386 Non ambiguous bp: Initial: 90037036 bp After Masking: 51755563 bp Masked: 42.52 % -- Input Database Coverage: 130074229 bp out of 2555444530 bp ( 5.09 % ) Sampling Time: 00:12:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2738970 Comparison Time: 02:42:02 (hh:mm:ss) Elapsed Time, 56729 HSPs Collected Number of families returned by RECON: 6117 Round Time: 02:58:41 (hh:mm:ss) Elapsed Time : 121 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 357578 repeats masked totaling 80763657 bp(s). - TE Masking time 00:06:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270014303 bp Num Contigs Represented = 1080 Non ambiguous bp: Initial: 270005419 bp After Masking: 150090169 bp Masked: 44.41 % -- Input Database Coverage: 400088532 bp out of 2555444530 bp ( 15.66 % ) Sampling Time: 00:36:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24559536 Comparison Time: 21:06:25 (hh:mm:ss) Elapsed Time, 185716 HSPs Collected Number of families returned by RECON: 26263 Round Time: 22:00:01 (hh:mm:ss) Elapsed Time : 274 families discovered. RepeatScout/RECON discovery complete: 613 families found Classification Time: 00:33:19 (hh:mm:ss) Elapsed Time Program Time: 26:59:19 (hh:mm:ss) Elapsed Time