RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.LZ3LMH/RM_349336.WedJul31016082024 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: 1720026966 Database = /dev/shm/rModeler.LZ3LMH/GCF_900408965.1_fSimDia1.1 - Sequences = 823 - Bases = 848827444 - N50 = 9636121 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 24944056-26725697 | [ 4 ] 23162416-24944056 | [ 1 ] 21380775-23162415 | [ ] 19599135-21380775 | [ 3 ] 17817494-19599134 | [ 3 ] 16035854-17817494 | [ 2 ] 14254213-16035853 | [ 3 ] 12472573-14254213 | [ 2 ] 10690932-12472572 | [ 3 ] 8909292-10690932 | [ 4 ] 7127651-8909291 | [ 7 ] 5346011-7127651 | [ 10 ] 3564370-5346010 |* [ 19 ] 1782730-3564370 |** [ 38 ] 1090-1782730 |************************************************** [ 724 ] Storage Throughput = excellent ( 1026.86 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40040053 bp ( 40038741 non ambiguous ) - Num Contigs Represented = 240 - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:57 (hh:mm:ss) Elapsed Time Round Time: 00:16:39 (hh:mm:ss) Elapsed Time : 591 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9968 repeats masked totaling 2133819 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10008461 bp Num Contigs Represented = 116 Non ambiguous bp: Initial: 10008215 bp After Masking: 7793250 bp Masked: 22.13 % -- Input Database Coverage: 10008461 bp out of 848827444 bp ( 1.18 % ) Sampling Time: 00:00:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:04:40 (hh:mm:ss) Elapsed Time, 6977 HSPs Collected Number of families returned by RECON: 1238 Round Time: 00:05:22 (hh:mm:ss) Elapsed Time : 22 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31244 repeats masked totaling 6695555 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30031512 bp Num Contigs Represented = 212 Non ambiguous bp: Initial: 30030446 bp After Masking: 23070085 bp Masked: 23.18 % -- Input Database Coverage: 40039973 bp out of 848827444 bp ( 4.72 % ) Sampling Time: 00:01:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 297606 Comparison Time: 00:22:30 (hh:mm:ss) Elapsed Time, 46362 HSPs Collected Number of families returned by RECON: 4541 Round Time: 00:25:10 (hh:mm:ss) Elapsed Time : 104 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 104365 repeats masked totaling 22187355 bp(s). - TE Masking time 00:01:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90017699 bp Num Contigs Represented = 314 Non ambiguous bp: Initial: 90012402 bp After Masking: 67040816 bp Masked: 25.52 % -- Input Database Coverage: 130057672 bp out of 848827444 bp ( 15.32 % ) Sampling Time: 00:04:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2627778 Comparison Time: 02:24:01 (hh:mm:ss) Elapsed Time, 250520 HSPs Collected Number of families returned by RECON: 15613 Round Time: 02:36:47 (hh:mm:ss) Elapsed Time : 411 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 366210 repeats masked totaling 78277598 bp(s). - TE Masking time 00:07:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270044906 bp Num Contigs Represented = 508 Non ambiguous bp: Initial: 270032667 bp After Masking: 189456276 bp Masked: 29.84 % -- Input Database Coverage: 400102578 bp out of 848827444 bp ( 47.14 % ) Sampling Time: 00:17:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23746386 Comparison Time: 15:51:09 (hh:mm:ss) Elapsed Time, 707756 HSPs Collected Number of families returned by RECON: 57334 Round Time: 17:02:02 (hh:mm:ss) Elapsed Time : 1023 families discovered. RepeatScout/RECON discovery complete: 2151 families found Classification Time: 01:22:11 (hh:mm:ss) Elapsed Time Program Time: 21:48:11 (hh:mm:ss) Elapsed Time