RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.lBRbV4/RM_3401333.ThuJul41409562024 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: 1720127396 Database = /dev/shm/rModeler.lBRbV4/GCF_036324505.1_JC_Emac_rtc_rv5 - Sequences = 27 - Bases = 606306633 Storage Throughput = good ( 978.08 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40050707 bp ( 40035207 non ambiguous ) - Num Contigs Represented = 24 - Sequence extraction : 00:00:43 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:50 (hh:mm:ss) Elapsed Time Round Time: 00:20:23 (hh:mm:ss) Elapsed Time : 267 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4377 repeats masked totaling 887842 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10042730 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10038230 bp After Masking: 8737477 bp Masked: 12.96 % -- Input Database Coverage: 10042730 bp out of 606306633 bp ( 1.66 % ) Sampling Time: 00:01:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:37 (hh:mm:ss) Elapsed Time, 9936 HSPs Collected Number of families returned by RECON: 1022 Round Time: 00:07:03 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15335 repeats masked totaling 3056129 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30048039 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 30037039 bp After Masking: 25851462 bp Masked: 13.93 % -- Input Database Coverage: 40090769 bp out of 606306633 bp ( 6.61 % ) Sampling Time: 00:03:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:28:46 (hh:mm:ss) Elapsed Time, 27659 HSPs Collected Number of families returned by RECON: 4005 Round Time: 00:33:04 (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 : 00:01:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49863 repeats masked totaling 9577725 bp(s). - TE Masking time 00:01:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90064012 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 90038512 bp After Masking: 76827613 bp Masked: 14.67 % -- Input Database Coverage: 130154781 bp out of 606306633 bp ( 21.47 % ) Sampling Time: 00:10:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 03:31:52 (hh:mm:ss) Elapsed Time, 167559 HSPs Collected Number of families returned by RECON: 14941 Round Time: 03:49:59 (hh:mm:ss) Elapsed Time : 315 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 196107 repeats masked totaling 39884826 bp(s). - TE Masking time 00:06:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270116536 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 270028948 bp After Masking: 219043788 bp Masked: 18.88 % -- Input Database Coverage: 400271317 bp out of 606306633 bp ( 66.02 % ) Sampling Time: 00:32:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22845420 Comparison Time: 23:40:00 (hh:mm:ss) Elapsed Time, 712809 HSPs Collected Number of families returned by RECON: 62457 Round Time: 25:21:04 (hh:mm:ss) Elapsed Time : 1001 families discovered. RepeatScout/RECON discovery complete: 1646 families found Classification Time: 01:25:57 (hh:mm:ss) Elapsed Time Program Time: 31:37:30 (hh:mm:ss) Elapsed Time