RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.CAN7dm/RM_1403552.SunJul200135132025 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: 1753000511 Database = /dev/shm/rModeler.CAN7dm/GCA_048772825.1_mCalLat2.hap2 - Sequences = 2820 - Bases = 3349745798 - N50 = 123789980 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 197677629-211797195 | [ 2 ] 183558064-197677629 | [ 1 ] 169438499-183558064 | [ 1 ] 155318933-169438498 | [ 2 ] 141199368-155318933 | [ ] 127079803-141199368 | [ 3 ] 112960238-127079803 | [ 2 ] 98840672-112960237 | [ 2 ] 84721107-98840672 | [ 2 ] 70601542-84721107 | [ 2 ] 56481977-70601542 | [ 1 ] 42362411-56481976 | [ ] 28242846-42362411 | [ 1 ] 14123281-28242846 | [ 3 ] 3716-14123281 |************************************************** [ 2798 ] Storage Throughput = excellent ( 1671.50 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40007063 bp ( 40005863 non ambiguous ) - Num Contigs Represented = 221 - Sequence extraction : 00:01:08 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:48 (hh:mm:ss) Elapsed Time Round Time: 00:13:06 (hh:mm:ss) Elapsed Time : 228 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 00:00:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11155 repeats masked totaling 2636795 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002265 bp Num Contigs Represented = 65 Non ambiguous bp: Initial: 10001865 bp After Masking: 7217875 bp Masked: 27.83 % -- Input Database Coverage: 10002265 bp out of 3349745798 bp ( 0.30 % ) Sampling Time: 00:00:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:02:58 (hh:mm:ss) Elapsed Time, 5897 HSPs Collected Number of families returned by RECON: 727 Round Time: 00:03:41 (hh:mm:ss) Elapsed Time : 22 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 37985 repeats masked totaling 9991676 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30004718 bp Num Contigs Represented = 192 Non ambiguous bp: Initial: 30003918 bp After Masking: 19373968 bp Masked: 35.43 % -- Input Database Coverage: 40006983 bp out of 3349745798 bp ( 1.19 % ) Sampling Time: 00:01:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 292995 Comparison Time: 00:12:06 (hh:mm:ss) Elapsed Time, 20548 HSPs Collected Number of families returned by RECON: 1897 Round Time: 00:14:07 (hh:mm:ss) Elapsed Time : 39 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 115039 repeats masked totaling 30878255 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90031966 bp Num Contigs Represented = 428 Non ambiguous bp: Initial: 90027866 bp After Masking: 56184681 bp Masked: 37.59 % -- Input Database Coverage: 130038949 bp out of 3349745798 bp ( 3.88 % ) Sampling Time: 00:05:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2604903 Comparison Time: 01:07:45 (hh:mm:ss) Elapsed Time, 92353 HSPs Collected Number of families returned by RECON: 7206 Round Time: 01:14:56 (hh:mm:ss) Elapsed Time : 172 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 382336 repeats masked totaling 106869569 bp(s). - TE Masking time 00:03:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270031352 bp Num Contigs Represented = 963 Non ambiguous bp: Initial: 270021052 bp After Masking: 156727806 bp Masked: 41.96 % -- Input Database Coverage: 400070301 bp out of 3349745798 bp ( 11.94 % ) Sampling Time: 00:16:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23574411 Comparison Time: 07:55:20 (hh:mm:ss) Elapsed Time, 710730 HSPs Collected Number of families returned by RECON: 28004 Round Time: 08:20:10 (hh:mm:ss) Elapsed Time : 369 families discovered. RepeatScout/RECON discovery complete: 830 families found Classification Time: 00:33:16 (hh:mm:ss) Elapsed Time Program Time: 10:39:16 (hh:mm:ss) Elapsed Time