RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.GaKQdn/RM_26475.SatNov252134192023 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: 1700976856 Database = /dev/shm/rModeler.GaKQdn/GCA_003957575.1_bCalAnn1_v1.h - Sequences = 3803 - Bases = 952083371 - N50 = 1477602 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 8922293-9559539 | [ 1 ] 8285047-8922292 | [ ] 7647802-8285047 | [ 2 ] 7010556-7647801 | [ ] 6373311-7010556 | [ 3 ] 5736065-6373310 | [ 2 ] 5098819-5736064 | [ 4 ] 4461574-5098819 | [ 4 ] 3824328-4461573 | [ 9 ] 3187083-3824328 | [ 25 ] 2549837-3187082 | [ 32 ] 1912591-2549836 | [ 40 ] 1275346-1912591 |* [ 79 ] 638100-1275345 |** [ 193 ] 855-638100 |************************************************* [ 3409 ] Storage Throughput = excellent ( 1209.75 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036674 bp ( 40036674 non ambiguous ) - Num Contigs Represented = 619 - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:23:52 (hh:mm:ss) Elapsed Time Round Time: 00:26:27 (hh:mm:ss) Elapsed Time : 82 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2908 repeats masked totaling 651926 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039972 bp Num Contigs Represented = 216 Non ambiguous bp: Initial: 10039972 bp After Masking: 9318694 bp Masked: 7.18 % -- Input Database Coverage: 10039972 bp out of 952083371 bp ( 1.05 % ) Sampling Time: 00:00:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 36585 Comparison Time: 00:08:56 (hh:mm:ss) Elapsed Time, 447 HSPs Collected Number of families returned by RECON: 264 Round Time: 00:09:31 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8640 repeats masked totaling 2085770 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30037844 bp Num Contigs Represented = 515 Non ambiguous bp: Initial: 30037844 bp After Masking: 27726170 bp Masked: 7.70 % -- Input Database Coverage: 40077816 bp out of 952083371 bp ( 4.21 % ) Sampling Time: 00:01:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 329266 Comparison Time: 00:42:39 (hh:mm:ss) Elapsed Time, 4338 HSPs Collected Number of families returned by RECON: 1813 Round Time: 00:44:21 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 25303 repeats masked totaling 5941871 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90036172 bp Num Contigs Represented = 1034 Non ambiguous bp: Initial: 90035672 bp After Masking: 83391667 bp Masked: 7.38 % -- Input Database Coverage: 130113988 bp out of 952083371 bp ( 13.67 % ) Sampling Time: 00:03:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3017196 Comparison Time: 05:24:36 (hh:mm:ss) Elapsed Time, 31564 HSPs Collected Number of families returned by RECON: 12068 Round Time: 05:31:15 (hh:mm:ss) Elapsed Time : 39 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 80924 repeats masked totaling 19390460 bp(s). - TE Masking time 00:02:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270038904 bp Num Contigs Represented = 1820 Non ambiguous bp: Initial: 270038904 bp After Masking: 248661138 bp Masked: 7.92 % -- Input Database Coverage: 400152892 bp out of 952083371 bp ( 42.03 % ) Sampling Time: 00:11:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 26524686 Comparison Time: 44:39:56 (hh:mm:ss) Elapsed Time, 217375 HSPs Collected Number of families returned by RECON: 80692 Round Time: 46:22:55 (hh:mm:ss) Elapsed Time : 200 families discovered. RepeatScout/RECON discovery complete: 330 families found Classification Time: 00:47:42 (hh:mm:ss) Elapsed Time Program Time: 54:02:11 (hh:mm:ss) Elapsed Time