RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.z7HwlN/RM_177355.SunNov170312172024 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: 1731841936 Database = /scratch/tmp/rModeler.z7HwlN/GCA_964212035.1_mMyoNat1.hap1.1 - Sequences = 343 - Bases = 2124021592 - N50 = 109845493 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 216310973-231761686 | [ 2 ] 200860261-216310973 | [ 1 ] 185409548-200860260 | [ ] 169958836-185409548 | [ ] 154508124-169958836 | [ ] 139057411-154508123 | [ 1 ] 123606699-139057411 | [ ] 108155986-123606698 | [ 2 ] 92705274-108155986 | [ 3 ] 77254562-92705274 | [ 4 ] 61803849-77254561 | [ 1 ] 46353137-61803849 | [ 4 ] 30902424-46353136 | [ 2 ] 15451712-30902424 | [ 3 ] 1000-15451712 |************************************************** [ 320 ] Storage Throughput = excellent ( 1411.81 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40022008 bp ( 40015408 non ambiguous ) - Num Contigs Represented = 33 - Sequence extraction : 00:01:18 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:46 (hh:mm:ss) Elapsed Time Round Time: 00:12:24 (hh:mm:ss) Elapsed Time : 404 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 00:00:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15472 repeats masked totaling 2966433 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10006327 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10004327 bp After Masking: 6576369 bp Masked: 34.26 % -- Input Database Coverage: 10006327 bp out of 2124021592 bp ( 0.47 % ) Sampling Time: 00:00:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:55 (hh:mm:ss) Elapsed Time, 4664 HSPs Collected Number of families returned by RECON: 796 Round Time: 00:03:43 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 48449 repeats masked totaling 9002214 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30015601 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 30011001 bp After Masking: 19910477 bp Masked: 33.66 % -- Input Database Coverage: 40021928 bp out of 2124021592 bp ( 1.88 % ) Sampling Time: 00:01:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:11:33 (hh:mm:ss) Elapsed Time, 20395 HSPs Collected Number of families returned by RECON: 2396 Round Time: 00:13:56 (hh:mm:ss) Elapsed Time : 54 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 152942 repeats masked totaling 28477401 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90027459 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 90012460 bp After Masking: 58179054 bp Masked: 35.37 % -- Input Database Coverage: 130049387 bp out of 2124021592 bp ( 6.12 % ) Sampling Time: 00:05:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2543640 Comparison Time: 01:18:29 (hh:mm:ss) Elapsed Time, 120419 HSPs Collected Number of families returned by RECON: 8610 Round Time: 01:26:12 (hh:mm:ss) Elapsed Time : 208 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 503402 repeats masked totaling 94338802 bp(s). - TE Masking time 00:02:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270051897 bp Num Contigs Represented = 104 Non ambiguous bp: Initial: 270015619 bp After Masking: 165275842 bp Masked: 38.79 % -- Input Database Coverage: 400101284 bp out of 2124021592 bp ( 18.84 % ) Sampling Time: 00:18:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22953700 Comparison Time: 08:06:17 (hh:mm:ss) Elapsed Time, 385175 HSPs Collected Number of families returned by RECON: 32262 Round Time: 08:35:06 (hh:mm:ss) Elapsed Time : 473 families discovered. RepeatScout/RECON discovery complete: 1152 families found Classification Time: 00:24:53 (hh:mm:ss) Elapsed Time Program Time: 10:56:14 (hh:mm:ss) Elapsed Time