RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.h5LXYE/RM_2403002.SunMar170507122024 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: 1710677232 Database = /dev/shm/rModeler.h5LXYE/GCA_036169615.1_bHelExo1.hap1 - Sequences = 131 - Bases = 1049650714 - N50 = 115481020 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 185011529-198225612 | [ 1 ] 171797446-185011528 | [ ] 158583364-171797446 | [ ] 145369281-158583363 | [ 1 ] 132155199-145369281 | [ ] 118941116-132155198 | [ ] 105727034-118941116 | [ 1 ] 92512951-105727033 | [ ] 79298869-92512951 | [ ] 66084786-79298868 | [ 1 ] 52870704-66084786 | [ ] 39656621-52870703 | [ 2 ] 26442539-39656621 |* [ 3 ] 13228456-26442538 |***** [ 12 ] 14374-13228456 |************************************************* [ 110 ] Storage Throughput = excellent ( 1202.72 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40037464 bp ( 40034164 non ambiguous ) - Num Contigs Represented = 46 - Sequence extraction : 00:01:42 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:37 (hh:mm:ss) Elapsed Time Round Time: 00:23:21 (hh:mm:ss) Elapsed Time : 97 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2636 repeats masked totaling 654588 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027775 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10026775 bp After Masking: 9204060 bp Masked: 8.21 % -- Input Database Coverage: 10027775 bp out of 1049650714 bp ( 0.96 % ) Sampling Time: 00:01:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:07:23 (hh:mm:ss) Elapsed Time, 896 HSPs Collected Number of families returned by RECON: 332 Round Time: 00:08:46 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7890 repeats masked totaling 2040734 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30009669 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 30007369 bp After Masking: 27356457 bp Masked: 8.83 % -- Input Database Coverage: 40037444 bp out of 1049650714 bp ( 3.81 % ) Sampling Time: 00:04:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:38:33 (hh:mm:ss) Elapsed Time, 4300 HSPs Collected Number of families returned by RECON: 1841 Round Time: 00:43:09 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 24247 repeats masked totaling 6154733 bp(s). - TE Masking time 00:00:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90017587 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 90009287 bp After Masking: 82027325 bp Masked: 8.87 % -- Input Database Coverage: 130055031 bp out of 1049650714 bp ( 12.39 % ) Sampling Time: 00:10:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 04:28:01 (hh:mm:ss) Elapsed Time, 44710 HSPs Collected Number of families returned by RECON: 12442 Round Time: 04:44:04 (hh:mm:ss) Elapsed Time : 67 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 82182 repeats masked totaling 21614422 bp(s). - TE Masking time 00:03:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270051819 bp Num Contigs Represented = 81 Non ambiguous bp: Initial: 270030922 bp After Masking: 243336770 bp Masked: 9.89 % -- Input Database Coverage: 400106850 bp out of 1049650714 bp ( 38.12 % ) Sampling Time: 00:33:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22892761 Comparison Time: 36:54:15 (hh:mm:ss) Elapsed Time, 248281 HSPs Collected Number of families returned by RECON: 83342 Round Time: 38:41:26 (hh:mm:ss) Elapsed Time : 191 families discovered. RepeatScout/RECON discovery complete: 365 families found Classification Time: 00:27:09 (hh:mm:ss) Elapsed Time Program Time: 45:07:55 (hh:mm:ss) Elapsed Time