RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.Q04f33/RM_2617694.TueApr220146112025 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: 1745311571 Database = /data/tmp/rModeler.Q04f33/GCA_041902795.1_ASM4190279v1 - Sequences = 460 - Bases = 833427914 - N50 = 33323679 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 42449230-45481281 | [ 2 ] 39417179-42449229 | [ 2 ] 36385128-39417178 | [ 2 ] 33353078-36385128 | [ 3 ] 30321027-33353077 | [ 2 ] 27288976-30321026 | [ 3 ] 24256925-27288975 | [ 2 ] 21224875-24256925 | [ 2 ] 18192824-21224874 | [ 4 ] 15160773-18192823 | [ 1 ] 12128722-15160772 | [ 3 ] 9096672-12128722 | [ ] 6064621-9096671 | [ ] 3032570-6064620 | [ 3 ] 520-3032570 |************************************************** [ 431 ] Storage Throughput = good ( 863.09 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40069228 bp ( 40025508 non ambiguous ) - Num Contigs Represented = 110 - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:31:14 (hh:mm:ss) Elapsed Time Round Time: 00:52:04 (hh:mm:ss) Elapsed Time : 366 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5321 repeats masked totaling 1835434 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10012752 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 10012752 bp After Masking: 6564276 bp Masked: 34.44 % -- Input Database Coverage: 10012752 bp out of 833427914 bp ( 1.20 % ) Sampling Time: 00:04:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:04:30 (hh:mm:ss) Elapsed Time, 10279 HSPs Collected Number of families returned by RECON: 679 Round Time: 00:09:23 (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 : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17353 repeats masked totaling 6153573 bp(s). - TE Masking time 00:01:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30056448 bp Num Contigs Represented = 98 Non ambiguous bp: Initial: 30012728 bp After Masking: 18496296 bp Masked: 38.37 % -- Input Database Coverage: 40069200 bp out of 833427914 bp ( 4.81 % ) Sampling Time: 00:09:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:21:41 (hh:mm:ss) Elapsed Time, 25670 HSPs Collected Number of families returned by RECON: 2601 Round Time: 00:35:08 (hh:mm:ss) Elapsed Time : 51 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:31:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 51231 repeats masked totaling 18483467 bp(s). - TE Masking time 00:03:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90320609 bp Num Contigs Represented = 142 Non ambiguous bp: Initial: 90022604 bp After Masking: 55215614 bp Masked: 38.66 % -- Input Database Coverage: 130389809 bp out of 833427914 bp ( 15.65 % ) Sampling Time: 00:36:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2582128 Comparison Time: 02:32:08 (hh:mm:ss) Elapsed Time, 180471 HSPs Collected Number of families returned by RECON: 9716 Round Time: 03:23:00 (hh:mm:ss) Elapsed Time : 257 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:39:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 188949 repeats masked totaling 64632914 bp(s). - TE Masking time 00:13:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270481844 bp Num Contigs Represented = 269 Non ambiguous bp: Initial: 270007565 bp After Masking: 156669650 bp Masked: 41.98 % -- Input Database Coverage: 400871653 bp out of 833427914 bp ( 48.10 % ) Sampling Time: 01:56:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23362030 Comparison Time: 16:34:14 (hh:mm:ss) Elapsed Time, 772958 HSPs Collected Number of families returned by RECON: 38281 Round Time: 20:04:09 (hh:mm:ss) Elapsed Time : 666 families discovered. RepeatScout/RECON discovery complete: 1347 families found Classification Time: 01:44:36 (hh:mm:ss) Elapsed Time Program Time: 26:48:20 (hh:mm:ss) Elapsed Time