RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.RWVpCy/RM_3448186.WedJun260036462024 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: 1719387406 Database = /dev/shm/rModeler.RWVpCy/GCF_949316205.1_fPlaFle2.1 - Sequences = 108 - Bases = 597120941 - N50 = 26771016 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 29241421-31329391 |* [ 2 ] 27153452-29241421 |**** [ 7 ] 25065483-27153452 |* [ 3 ] 22977514-25065483 |** [ 4 ] 20889545-22977514 |** [ 4 ] 18801576-20889545 | [ 1 ] 16713607-18801576 | [ 1 ] 14625638-16713607 |* [ 2 ] 12537669-14625638 | [ ] 10449700-12537669 | [ ] 8361731-10449700 | [ ] 6273762-8361731 | [ ] 4185793-6273762 | [ ] 2097824-4185793 | [ ] 9855-2097824 |************************************************** [ 84 ] Storage Throughput = good ( 880.40 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40008831 bp ( 40001431 non ambiguous ) - Num Contigs Represented = 30 - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:28 (hh:mm:ss) Elapsed Time Round Time: 00:21:20 (hh:mm:ss) Elapsed Time : 283 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5710 repeats masked totaling 1086983 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003085 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10001285 bp After Masking: 8619529 bp Masked: 13.82 % -- Input Database Coverage: 10003085 bp out of 597120941 bp ( 1.68 % ) Sampling Time: 00:00:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:55 (hh:mm:ss) Elapsed Time, 5907 HSPs Collected Number of families returned by RECON: 1192 Round Time: 00:06:53 (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 : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18724 repeats masked totaling 3041960 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30005666 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 30000066 bp After Masking: 26134002 bp Masked: 12.89 % -- Input Database Coverage: 40008751 bp out of 597120941 bp ( 6.70 % ) Sampling Time: 00:02:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:30:33 (hh:mm:ss) Elapsed Time, 90895 HSPs Collected Number of families returned by RECON: 4991 Round Time: 00:34:07 (hh:mm:ss) Elapsed Time : 90 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 66623 repeats masked totaling 11103721 bp(s). - TE Masking time 00:01:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90034230 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 90018630 bp After Masking: 75916688 bp Masked: 15.67 % -- Input Database Coverage: 130042981 bp out of 597120941 bp ( 21.78 % ) Sampling Time: 00:07:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 03:24:24 (hh:mm:ss) Elapsed Time, 752578 HSPs Collected Number of families returned by RECON: 18805 Round Time: 03:40:44 (hh:mm:ss) Elapsed Time : 330 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 251637 repeats masked totaling 43312577 bp(s). - TE Masking time 00:06:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270079653 bp Num Contigs Represented = 76 Non ambiguous bp: Initial: 270036544 bp After Masking: 218620298 bp Masked: 19.04 % -- Input Database Coverage: 400122634 bp out of 597120941 bp ( 67.01 % ) Sampling Time: 00:23:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22946925 Comparison Time: 27:01:20 (hh:mm:ss) Elapsed Time, 8303212 HSPs Collected Number of families returned by RECON: 78167 Round Time: 29:07:02 (hh:mm:ss) Elapsed Time : 853 families discovered. RepeatScout/RECON discovery complete: 1568 families found Classification Time: 01:17:35 (hh:mm:ss) Elapsed Time Program Time: 35:07:41 (hh:mm:ss) Elapsed Time