RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.u9D9f1/RM_2127709.WedNov292246062023 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: 1701326765 Database = /dev/shm/rModeler.u9D9f1/GCF_029931775.1_rEulEur1.hap1 - Sequences = 591 - Bases = 1781916107 - N50 = 109329079 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 171272383-183506054 | [ 1 ] 159038713-171272383 | [ ] 146805043-159038713 | [ ] 134571372-146805042 | [ 1 ] 122337702-134571372 | [ 2 ] 110104032-122337702 | [ 1 ] 97870362-110104032 | [ 3 ] 85636691-97870361 | [ 1 ] 73403021-85636691 | [ 2 ] 61169351-73403021 | [ 3 ] 48935681-61169351 | [ 3 ] 36702010-48935680 | [ 2 ] 24468340-36702010 | [ 1 ] 12234670-24468340 | [ 1 ] 1000-12234670 |************************************************** [ 570 ] Storage Throughput = excellent ( 1421.88 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40126548 bp ( 40012454 non ambiguous ) - Num Contigs Represented = 39 - Sequence extraction : 00:01:57 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:11:41 (hh:mm:ss) Elapsed Time Round Time: 00:21:00 (hh:mm:ss) Elapsed Time : 604 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21067 repeats masked totaling 3840248 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10021113 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10020913 bp After Masking: 6068396 bp Masked: 39.44 % -- Input Database Coverage: 10021113 bp out of 1781916107 bp ( 0.56 % ) Sampling Time: 00:01:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:25 (hh:mm:ss) Elapsed Time, 8000 HSPs Collected Number of families returned by RECON: 1334 Round Time: 00:07:03 (hh:mm:ss) Elapsed Time : 24 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 64021 repeats masked totaling 11864063 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30145435 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 30031541 bp After Masking: 17722507 bp Masked: 40.99 % -- Input Database Coverage: 40166548 bp out of 1781916107 bp ( 2.25 % ) Sampling Time: 00:04:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:25:48 (hh:mm:ss) Elapsed Time, 47258 HSPs Collected Number of families returned by RECON: 4351 Round Time: 00:32:02 (hh:mm:ss) Elapsed Time : 118 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 203202 repeats masked totaling 37043709 bp(s). - TE Masking time 00:01:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90213922 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 90008828 bp After Masking: 51466355 bp Masked: 42.82 % -- Input Database Coverage: 130380470 bp out of 1781916107 bp ( 7.32 % ) Sampling Time: 00:14:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2577585 Comparison Time: 02:34:01 (hh:mm:ss) Elapsed Time, 223608 HSPs Collected Number of families returned by RECON: 13389 Round Time: 02:57:52 (hh:mm:ss) Elapsed Time : 500 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 681484 repeats masked totaling 124054061 bp(s). - TE Masking time 00:08:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270594487 bp Num Contigs Represented = 138 Non ambiguous bp: Initial: 270036910 bp After Masking: 141931345 bp Masked: 47.44 % -- Input Database Coverage: 400974957 bp out of 1781916107 bp ( 22.50 % ) Sampling Time: 00:49:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23211891 Comparison Time: 16:54:40 (hh:mm:ss) Elapsed Time, 564951 HSPs Collected Number of families returned by RECON: 40093 Round Time: 18:43:31 (hh:mm:ss) Elapsed Time : 1197 families discovered. RepeatScout/RECON discovery complete: 2443 families found Classification Time: 01:24:18 (hh:mm:ss) Elapsed Time Program Time: 24:05:46 (hh:mm:ss) Elapsed Time