RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.BU7nPs/RM_3441078.FriJul181030002025 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: 1752859799 Database = /dev/shm/rModeler.BU7nPs/GCA_048127045.1_DamDam1_v1.pat - Sequences = 310 - Bases = 2380677270 - N50 = 77054116 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 119068543-127573368 | [ 1 ] 110563718-119068542 | [ 2 ] 102058894-110563718 | [ 1 ] 93554069-102058893 | [ 2 ] 85049245-93554069 | [ 2 ] 76544420-85049244 | [ 5 ] 68039596-76544420 | [ 1 ] 59534771-68039595 |* [ 7 ] 51029947-59534771 |* [ 6 ] 42525122-51029946 | [ 4 ] 34020298-42525122 | [ 2 ] 25515473-34020297 | [ ] 17010649-25515473 | [ ] 8505824-17010648 | [ ] 1000-8505824 |************************************************** [ 277 ] Storage Throughput = excellent ( 1184.14 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40032306 bp ( 40031706 non ambiguous ) - Num Contigs Represented = 58 - Sequence extraction : 00:01:30 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:01 (hh:mm:ss) Elapsed Time Round Time: 00:30:05 (hh:mm:ss) Elapsed Time : 248 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13469 repeats masked totaling 3012434 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003710 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 10003610 bp After Masking: 6828821 bp Masked: 31.74 % -- Input Database Coverage: 10003710 bp out of 2380677270 bp ( 0.42 % ) Sampling Time: 00:01:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:04:41 (hh:mm:ss) Elapsed Time, 5369 HSPs Collected Number of families returned by RECON: 749 Round Time: 00:06:04 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43909 repeats masked totaling 9784222 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30028592 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 30028092 bp After Masking: 19725121 bp Masked: 34.31 % -- Input Database Coverage: 40032302 bp out of 2380677270 bp ( 1.68 % ) Sampling Time: 00:03:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:25:49 (hh:mm:ss) Elapsed Time, 17763 HSPs Collected Number of families returned by RECON: 2130 Round Time: 00:29:51 (hh:mm:ss) Elapsed Time : 55 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 137325 repeats masked totaling 30912275 bp(s). - TE Masking time 00:01:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90007685 bp Num Contigs Represented = 79 Non ambiguous bp: Initial: 90006785 bp After Masking: 57544974 bp Masked: 36.07 % -- Input Database Coverage: 130039987 bp out of 2380677270 bp ( 5.46 % ) Sampling Time: 00:10:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 03:08:54 (hh:mm:ss) Elapsed Time, 78896 HSPs Collected Number of families returned by RECON: 7762 Round Time: 03:22:13 (hh:mm:ss) Elapsed Time : 176 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 450044 repeats masked totaling 99402052 bp(s). - TE Masking time 00:06:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270027854 bp Num Contigs Represented = 129 Non ambiguous bp: Initial: 270025154 bp After Masking: 166384200 bp Masked: 38.38 % -- Input Database Coverage: 400067841 bp out of 2380677270 bp ( 16.80 % ) Sampling Time: 00:31:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22892761 Comparison Time: 24:50:54 (hh:mm:ss) Elapsed Time, 209882 HSPs Collected Number of families returned by RECON: 33248 Round Time: 25:48:25 (hh:mm:ss) Elapsed Time : 369 families discovered. RepeatScout/RECON discovery complete: 866 families found Classification Time: 00:35:03 (hh:mm:ss) Elapsed Time Program Time: 30:51:41 (hh:mm:ss) Elapsed Time