RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.mdoQ4M/RM_21277.MonNov271304282023 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: 1701119067 Database = /dev/shm/rModeler.mdoQ4M/GCF_963584025.1_fLabMix1.1 - Sequences = 324 - Bases = 740563171 - N50 = 30722800 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 34497858-36961920 | [ 3 ] 32033797-34497858 | [ 4 ] 29569736-32033797 |* [ 6 ] 27105674-29569735 | [ 3 ] 24641613-27105674 | [ 5 ] 22177552-24641613 | [ ] 19713490-22177551 | [ 2 ] 17249429-19713490 | [ ] 14785368-17249429 | [ ] 12321306-14785367 | [ 1 ] 9857245-12321306 | [ ] 7393184-9857245 | [ ] 4929122-7393183 | [ ] 2465061-4929122 | [ ] 1000-2465061 |************************************************** [ 300 ] Storage Throughput = excellent ( 1132.12 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40027723 bp ( 40022723 non ambiguous ) - Num Contigs Represented = 72 - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:25:44 (hh:mm:ss) Elapsed Time Round Time: 00:32:06 (hh:mm:ss) Elapsed Time : 438 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 00:03:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7220 repeats masked totaling 1145896 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002310 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 10000910 bp After Masking: 7819396 bp Masked: 21.81 % -- Input Database Coverage: 10002310 bp out of 740563171 bp ( 1.35 % ) Sampling Time: 00:04:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:06:07 (hh:mm:ss) Elapsed Time, 5169 HSPs Collected Number of families returned by RECON: 1158 Round Time: 00:10:31 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22938 repeats masked totaling 3765844 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30025410 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 30021810 bp After Masking: 22892070 bp Masked: 23.75 % -- Input Database Coverage: 40027720 bp out of 740563171 bp ( 5.41 % ) Sampling Time: 00:10:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:32:47 (hh:mm:ss) Elapsed Time, 41234 HSPs Collected Number of families returned by RECON: 4256 Round Time: 00:45:28 (hh:mm:ss) Elapsed Time : 108 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 00:34:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 77929 repeats masked totaling 12676230 bp(s). - TE Masking time 00:01:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90032032 bp Num Contigs Represented = 115 Non ambiguous bp: Initial: 90017832 bp After Masking: 67276784 bp Masked: 25.26 % -- Input Database Coverage: 130059752 bp out of 740563171 bp ( 17.56 % ) Sampling Time: 00:38:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2568511 Comparison Time: 03:50:29 (hh:mm:ss) Elapsed Time, 237459 HSPs Collected Number of families returned by RECON: 14970 Round Time: 04:38:59 (hh:mm:ss) Elapsed Time : 414 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:45:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 288993 repeats masked totaling 48794034 bp(s). - TE Masking time 00:08:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270053639 bp Num Contigs Represented = 201 Non ambiguous bp: Initial: 270013039 bp After Masking: 190343106 bp Masked: 29.51 % -- Input Database Coverage: 400113391 bp out of 740563171 bp ( 54.03 % ) Sampling Time: 01:58:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23252790 Comparison Time: 30:01:29 (hh:mm:ss) Elapsed Time, 660388 HSPs Collected Number of families returned by RECON: 58690 Round Time: 33:34:13 (hh:mm:ss) Elapsed Time : 967 families discovered. RepeatScout/RECON discovery complete: 1939 families found Classification Time: 01:21:10 (hh:mm:ss) Elapsed Time Program Time: 41:02:27 (hh:mm:ss) Elapsed Time