RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.GM4EDp/RM_3764051.FriJul181028522025 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: 1752859732 Database = /dev/shm/rModeler.GM4EDp/GCA_047511595.1_fPolLow2.hap2 - Sequences = 199 - Bases = 671709512 - N50 = 28798184 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 36133217-38713300 | [ 1 ] 33553135-36133217 | [ 2 ] 30973052-33553134 | [ 2 ] 28392970-30973052 |** [ 7 ] 25812887-28392969 |* [ 5 ] 23232805-25812887 | [ 2 ] 20652722-23232804 | [ 2 ] 18072640-20652722 | [ 2 ] 15492557-18072639 | [ 1 ] 12912475-15492557 | [ ] 10332392-12912474 | [ ] 7752310-10332392 | [ ] 5172227-7752309 | [ ] 2592145-5172227 | [ ] 12063-2592145 |************************************************** [ 175 ] Storage Throughput = excellent ( 1140.09 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40012665 bp ( 40003665 non ambiguous ) - Num Contigs Represented = 35 - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:48 (hh:mm:ss) Elapsed Time Round Time: 00:27:54 (hh:mm:ss) Elapsed Time : 542 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6329 repeats masked totaling 901365 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10021101 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10018501 bp After Masking: 8062918 bp Masked: 19.52 % -- Input Database Coverage: 10021101 bp out of 671709512 bp ( 1.49 % ) Sampling Time: 00:01:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:15 (hh:mm:ss) Elapsed Time, 6492 HSPs Collected Number of families returned by RECON: 1598 Round Time: 00:07:31 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20377 repeats masked totaling 2778973 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30031540 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 30025140 bp After Masking: 23980324 bp Masked: 20.13 % -- Input Database Coverage: 40052641 bp out of 671709512 bp ( 5.96 % ) Sampling Time: 00:06:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:31:00 (hh:mm:ss) Elapsed Time, 47307 HSPs Collected Number of families returned by RECON: 6154 Round Time: 00:39:13 (hh:mm:ss) Elapsed Time : 121 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 73141 repeats masked totaling 10383784 bp(s). - TE Masking time 00:01:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90049290 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 90028490 bp After Masking: 70277608 bp Masked: 21.94 % -- Input Database Coverage: 130101931 bp out of 671709512 bp ( 19.37 % ) Sampling Time: 00:17:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 03:52:04 (hh:mm:ss) Elapsed Time, 367327 HSPs Collected Number of families returned by RECON: 20725 Round Time: 04:29:13 (hh:mm:ss) Elapsed Time : 556 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:45:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 297185 repeats masked totaling 47014669 bp(s). - TE Masking time 00:11:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270066326 bp Num Contigs Represented = 130 Non ambiguous bp: Initial: 270003809 bp After Masking: 194706991 bp Masked: 27.89 % -- Input Database Coverage: 400168257 bp out of 671709512 bp ( 59.57 % ) Sampling Time: 01:01:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23001153 Comparison Time: 29:07:05 (hh:mm:ss) Elapsed Time, 988950 HSPs Collected Number of families returned by RECON: 69488 Round Time: 32:29:13 (hh:mm:ss) Elapsed Time : 1295 families discovered. RepeatScout/RECON discovery complete: 2525 families found Classification Time: 01:45:00 (hh:mm:ss) Elapsed Time Program Time: 39:58:04 (hh:mm:ss) Elapsed Time