RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.G1uDAB/RM_20759.SunJul71527582024 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: 1720391277 Database = /dev/shm/rModeler.G1uDAB/GCF_001515605.1_SAMN03320099.WGS_v1.1 - Sequences = 85682 - Bases = 1632718266 - N50 = 1284251 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 6676878-7153784 | [ 1 ] 6199972-6676877 | [ ] 5723067-6199972 | [ 3 ] 5246161-5723066 | [ 4 ] 4769256-5246161 | [ 1 ] 4292350-4769255 | [ 6 ] 3815444-4292349 | [ 8 ] 3338539-3815444 | [ 22 ] 2861633-3338538 | [ 29 ] 2384728-2861633 | [ 46 ] 1907822-2384727 | [ 71 ] 1430916-1907821 | [ 119 ] 954011-1430916 | [ 221 ] 477105-954010 | [ 440 ] 200-477105 |************************************************** [ 84711 ] Storage Throughput = excellent ( 1159.17 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 43142355 bp ( 40021070 non ambiguous ) - Num Contigs Represented = 2888 - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:27 (hh:mm:ss) Elapsed Time Round Time: 00:27:37 (hh:mm:ss) Elapsed Time : 1332 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 00:00:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19019 repeats masked totaling 2655355 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10680568 bp Num Contigs Represented = 798 Non ambiguous bp: Initial: 10001631 bp After Masking: 7141809 bp Masked: 28.59 % -- Input Database Coverage: 10680568 bp out of 1632718266 bp ( 0.65 % ) Sampling Time: 00:01:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 348195 Comparison Time: 00:09:00 (hh:mm:ss) Elapsed Time, 14082 HSPs Collected Number of families returned by RECON: 1910 Round Time: 00:10:51 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 58188 repeats masked totaling 8232541 bp(s). - TE Masking time 00:01:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 32461707 bp Num Contigs Represented = 2204 Non ambiguous bp: Initial: 30019359 bp After Masking: 21261718 bp Masked: 29.17 % -- Input Database Coverage: 43142275 bp out of 1632718266 bp ( 2.64 % ) Sampling Time: 00:02:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2985346 Comparison Time: 00:43:54 (hh:mm:ss) Elapsed Time, 69369 HSPs Collected Number of families returned by RECON: 6480 Round Time: 00:49:48 (hh:mm:ss) Elapsed Time : 174 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 192137 repeats masked totaling 27451153 bp(s). - TE Masking time 00:04:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 96969554 bp Num Contigs Represented = 6170 Non ambiguous bp: Initial: 90034269 bp After Masking: 60985451 bp Masked: 32.26 % -- Input Database Coverage: 140111829 bp out of 1632718266 bp ( 8.58 % ) Sampling Time: 00:09:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 27621028 Comparison Time: 04:41:24 (hh:mm:ss) Elapsed Time, 390831 HSPs Collected Number of families returned by RECON: 19078 Round Time: 05:11:50 (hh:mm:ss) Elapsed Time : 758 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 663631 repeats masked totaling 97593300 bp(s). - TE Masking time 00:21:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 291137965 bp Num Contigs Represented = 16636 Non ambiguous bp: Initial: 270005157 bp After Masking: 167565886 bp Masked: 37.94 % -- Input Database Coverage: 431249794 bp out of 1632718266 bp ( 26.41 % ) Sampling Time: 00:36:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 243509346 Comparison Time: 34:41:41 (hh:mm:ss) Elapsed Time, 920052 HSPs Collected Number of families returned by RECON: 65374 Round Time: 37:39:45 (hh:mm:ss) Elapsed Time : 1492 families discovered. RepeatScout/RECON discovery complete: 3773 families found Classification Time: 02:00:40 (hh:mm:ss) Elapsed Time Program Time: 46:20:31 (hh:mm:ss) Elapsed Time