RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ifNo6G/RM_90312.MonJan91610262023 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: 1673309425 Database = /dev/shm/rModeler.ifNo6G/GCF_017639655.2_bFalNau1.pat - Sequences = 291 - Bases = 1215719661 - N50 = 92799756 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 118944776-127440759 | [ 3 ] 110448794-118944776 | [ 1 ] 101952812-110448794 | [ ] 93456829-101952811 | [ ] 84960847-93456829 | [ 3 ] 76464865-84960847 | [ ] 67968883-76464865 | [ 1 ] 59472900-67968882 | [ 1 ] 50976918-59472900 | [ 1 ] 42480936-50976918 | [ ] 33984954-42480936 | [ 2 ] 25488971-33984953 | [ 3 ] 16992989-25488971 | [ 2 ] 8497007-16992989 | [ ] 1025-8497007 |************************************************* [ 274 ] Storage Throughput = excellent ( 1048.27 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40090249 bp ( 40005186 non ambiguous ) - Num Contigs Represented = 39 - Sequence extraction : 00:02:35 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:47 (hh:mm:ss) Elapsed Time Round Time: 00:21:44 (hh:mm:ss) Elapsed Time : 74 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:40 (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... 1396 repeats masked totaling 447835 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10033703 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 10033603 bp After Masking: 9417790 bp Masked: 6.14 % -- Input Database Coverage: 10033703 bp out of 1215719661 bp ( 0.83 % ) Sampling Time: 00:01:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:08:33 (hh:mm:ss) Elapsed Time, 521 HSPs Collected Number of families returned by RECON: 258 Round Time: 00:10:04 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4362 repeats masked totaling 1428301 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30096546 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 30011583 bp After Masking: 28367379 bp Masked: 5.48 % -- Input Database Coverage: 40130249 bp out of 1215719661 bp ( 3.30 % ) Sampling Time: 00:03:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:44:54 (hh:mm:ss) Elapsed Time, 5367 HSPs Collected Number of families returned by RECON: 1584 Round Time: 00:49:01 (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 : 00:05:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14511 repeats masked totaling 4577573 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90305048 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 90011886 bp After Masking: 84719117 bp Masked: 5.88 % -- Input Database Coverage: 130435297 bp out of 1215719661 bp ( 10.73 % ) Sampling Time: 00:12:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2573046 Comparison Time: 05:36:55 (hh:mm:ss) Elapsed Time, 43344 HSPs Collected Number of families returned by RECON: 9864 Round Time: 05:52:56 (hh:mm:ss) Elapsed Time : 73 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:16:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 54739 repeats masked totaling 16294118 bp(s). - TE Masking time 00:02:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270845048 bp Num Contigs Represented = 114 Non ambiguous bp: Initial: 270003088 bp After Masking: 251751336 bp Masked: 6.76 % -- Input Database Coverage: 401280345 bp out of 1215719661 bp ( 33.01 % ) Sampling Time: 00:35:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23137003 Comparison Time: 41:32:51 (hh:mm:ss) Elapsed Time, 222600 HSPs Collected Number of families returned by RECON: 63498 Round Time: 42:57:33 (hh:mm:ss) Elapsed Time : 234 families discovered. RepeatScout/RECON discovery complete: 390 families found Classification Time: 00:55:19 (hh:mm:ss) Elapsed Time Program Time: 51:06:37 (hh:mm:ss) Elapsed Time