RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.I7JyOc/RM_43300.SunMay71059482023 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: 1683482385 Database = /dev/shm/rModeler.I7JyOc/GCA_020745735.1_sHemOce1.pat.X.cur. - Sequences = 1963 - Bases = 3983483121 - N50 = 84986831 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 156391190-167561909 | [ 1 ] 145220472-156391190 | [ 2 ] 134049753-145220471 | [ 2 ] 122879035-134049753 | [ 2 ] 111708316-122879034 | [ 3 ] 100537598-111708316 | [ 2 ] 89366879-100537597 | [ 2 ] 78196161-89366879 | [ 4 ] 67025442-78196160 | [ 3 ] 55854724-67025442 | [ 8 ] 44684005-55854723 | [ 7 ] 33513287-44684005 | [ 5 ] 22342568-33513286 | [ 5 ] 11171850-22342568 | [ 4 ] 1132-11171850 |************************************************** [ 1913 ] Storage Throughput = excellent ( 1571.42 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40872580 bp ( 40001074 non ambiguous ) - Num Contigs Represented = 155 - Sequence extraction : 00:01:18 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:22 (hh:mm:ss) Elapsed Time Round Time: 00:18:31 (hh:mm:ss) Elapsed Time : 524 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21347 repeats masked totaling 5355374 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10262296 bp Num Contigs Represented = 77 Non ambiguous bp: Initial: 10035292 bp After Masking: 4055296 bp Masked: 59.59 % -- Input Database Coverage: 10262296 bp out of 3983483121 bp ( 0.26 % ) Sampling Time: 00:02:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33411 Comparison Time: 00:10:08 (hh:mm:ss) Elapsed Time, 4440 HSPs Collected Number of families returned by RECON: 709 Round Time: 00:12:37 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 65873 repeats masked totaling 16514411 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30650346 bp Num Contigs Represented = 129 Non ambiguous bp: Initial: 30005844 bp After Masking: 11672899 bp Masked: 61.10 % -- Input Database Coverage: 40912642 bp out of 3983483121 bp ( 1.03 % ) Sampling Time: 00:05:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 299151 Comparison Time: 00:30:44 (hh:mm:ss) Elapsed Time, 25869 HSPs Collected Number of families returned by RECON: 2277 Round Time: 00:37:31 (hh:mm:ss) Elapsed Time : 56 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 206052 repeats masked totaling 51224590 bp(s). - TE Masking time 00:01:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91708876 bp Num Contigs Represented = 287 Non ambiguous bp: Initial: 90016106 bp After Masking: 33607055 bp Masked: 62.67 % -- Input Database Coverage: 132621518 bp out of 3983483121 bp ( 3.33 % ) Sampling Time: 00:20:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2706301 Comparison Time: 02:15:46 (hh:mm:ss) Elapsed Time, 401165 HSPs Collected Number of families returned by RECON: 6970 Round Time: 02:42:06 (hh:mm:ss) Elapsed Time : 263 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:43:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 669314 repeats masked totaling 164904992 bp(s). - TE Masking time 00:06:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 275625069 bp Num Contigs Represented = 575 Non ambiguous bp: Initial: 270004338 bp After Masking: 89998439 bp Masked: 66.67 % -- Input Database Coverage: 408246587 bp out of 3983483121 bp ( 10.25 % ) Sampling Time: 00:58:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24175581 Comparison Time: 13:09:00 (hh:mm:ss) Elapsed Time, 873823 HSPs Collected Number of families returned by RECON: 18807 Round Time: 14:23:47 (hh:mm:ss) Elapsed Time : 673 families discovered. RepeatScout/RECON discovery complete: 1527 families found Classification Time: 00:50:25 (hh:mm:ss) Elapsed Time Program Time: 19:04:57 (hh:mm:ss) Elapsed Time