RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.pTYEtB/RM_4127664.WedApr161306262025 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: 1744833980 Database = /dev/shm/rModeler.pTYEtB/GCA_965115945.1_mMyoEma1.hap2.1 - Sequences = 504 - Bases = 2081394546 - N50 = 108920819 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 209134860-224072993 | [ 2 ] 194196727-209134859 | [ 1 ] 179258594-194196726 | [ ] 164320461-179258593 | [ ] 149382328-164320460 | [ ] 134444195-149382327 | [ ] 119506062-134444194 | [ 1 ] 104567930-119506062 | [ 2 ] 89629797-104567929 | [ 3 ] 74691664-89629796 | [ 2 ] 59753531-74691663 | [ 2 ] 44815398-59753530 | [ 5 ] 29877265-44815397 | [ 1 ] 14939132-29877264 | [ 2 ] 1000-14939132 |************************************************** [ 483 ] Storage Throughput = excellent ( 1710.41 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40038706 bp ( 40032106 non ambiguous ) - Num Contigs Represented = 75 - Sequence extraction : 00:01:13 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:28 (hh:mm:ss) Elapsed Time Round Time: 00:12:50 (hh:mm:ss) Elapsed Time : 352 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13076 repeats masked totaling 2664112 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040182 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 10038982 bp After Masking: 6508508 bp Masked: 35.17 % -- Input Database Coverage: 10040182 bp out of 2081394546 bp ( 0.48 % ) Sampling Time: 00:00:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:06 (hh:mm:ss) Elapsed Time, 4677 HSPs Collected Number of families returned by RECON: 756 Round Time: 00:03:54 (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 : 00:00:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 42335 repeats masked totaling 8233359 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30038528 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 30033128 bp After Masking: 19405147 bp Masked: 35.39 % -- Input Database Coverage: 40078710 bp out of 2081394546 bp ( 1.93 % ) Sampling Time: 00:01:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:12:55 (hh:mm:ss) Elapsed Time, 23683 HSPs Collected Number of families returned by RECON: 2517 Round Time: 00:15:17 (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 : 00:02:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 134371 repeats masked totaling 26048424 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90049414 bp Num Contigs Represented = 122 Non ambiguous bp: Initial: 90035985 bp After Masking: 58047257 bp Masked: 35.53 % -- Input Database Coverage: 130128124 bp out of 2081394546 bp ( 6.25 % ) Sampling Time: 00:06:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 01:11:08 (hh:mm:ss) Elapsed Time, 109071 HSPs Collected Number of families returned by RECON: 9033 Round Time: 01:19:05 (hh:mm:ss) Elapsed Time : 230 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 456517 repeats masked totaling 87602482 bp(s). - TE Masking time 00:02:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270045233 bp Num Contigs Represented = 220 Non ambiguous bp: Initial: 270003048 bp After Masking: 163630047 bp Masked: 39.40 % -- Input Database Coverage: 400173357 bp out of 2081394546 bp ( 19.23 % ) Sampling Time: 00:20:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23055445 Comparison Time: 07:55:34 (hh:mm:ss) Elapsed Time, 257377 HSPs Collected Number of families returned by RECON: 32834 Round Time: 08:24:55 (hh:mm:ss) Elapsed Time : 454 families discovered. RepeatScout/RECON discovery complete: 1103 families found Classification Time: 00:20:39 (hh:mm:ss) Elapsed Time Program Time: 10:36:40 (hh:mm:ss) Elapsed Time