RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.GmYdSS/RM_3673486.SatNov252133112023 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: 1700976788 Database = /dev/shm/rModeler.GmYdSS/GCF_963259705.1_mMyoDau2.1 - Sequences = 121 - Bases = 2127807131 - N50 = 111432089 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 218504744-234112155 |* [ 3 ] 202897334-218504744 | [ ] 187289924-202897334 | [ ] 171682513-187289923 | [ ] 156075103-171682513 | [ ] 140467693-156075103 | [ ] 124860282-140467692 | [ 1 ] 109252872-124860282 |* [ 2 ] 93645462-109252872 |* [ 3 ] 78038051-93645461 |** [ 4 ] 62430641-78038051 | [ 1 ] 46823231-62430641 |** [ 4 ] 31215820-46823230 | [ 1 ] 15608410-31215820 |** [ 4 ] 1000-15608410 |************************************************** [ 98 ] Storage Throughput = excellent ( 1171.56 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40007565 bp ( 40004765 non ambiguous ) - Num Contigs Represented = 34 - Sequence extraction : 00:02:21 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:57 (hh:mm:ss) Elapsed Time Round Time: 00:24:30 (hh:mm:ss) Elapsed Time : 382 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 00:00:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15020 repeats masked totaling 2710746 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001109 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10000709 bp After Masking: 6838431 bp Masked: 31.62 % -- Input Database Coverage: 10001109 bp out of 2127807131 bp ( 0.47 % ) Sampling Time: 00:01:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:08:51 (hh:mm:ss) Elapsed Time, 6181 HSPs Collected Number of families returned by RECON: 781 Round Time: 00:10:33 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 47996 repeats masked totaling 8670529 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30006376 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 30003976 bp After Masking: 19834510 bp Masked: 33.89 % -- Input Database Coverage: 40007485 bp out of 2127807131 bp ( 1.88 % ) Sampling Time: 00:04:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:26:58 (hh:mm:ss) Elapsed Time, 25725 HSPs Collected Number of families returned by RECON: 2547 Round Time: 00:32:14 (hh:mm:ss) Elapsed Time : 52 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 153905 repeats masked totaling 28136170 bp(s). - TE Masking time 00:01:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90018784 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 90005984 bp After Masking: 57755096 bp Masked: 35.83 % -- Input Database Coverage: 130026269 bp out of 2127807131 bp ( 6.11 % ) Sampling Time: 00:12:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2543640 Comparison Time: 02:48:40 (hh:mm:ss) Elapsed Time, 130146 HSPs Collected Number of families returned by RECON: 8150 Round Time: 03:04:32 (hh:mm:ss) Elapsed Time : 204 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:19:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 493504 repeats masked totaling 91622194 bp(s). - TE Masking time 00:06:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270063197 bp Num Contigs Represented = 67 Non ambiguous bp: Initial: 270036539 bp After Masking: 165329221 bp Masked: 38.78 % -- Input Database Coverage: 400089466 bp out of 2127807131 bp ( 18.80 % ) Sampling Time: 00:40:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22818390 Comparison Time: 21:26:13 (hh:mm:ss) Elapsed Time, 406153 HSPs Collected Number of families returned by RECON: 34345 Round Time: 22:30:06 (hh:mm:ss) Elapsed Time : 519 families discovered. RepeatScout/RECON discovery complete: 1167 families found Classification Time: 00:44:55 (hh:mm:ss) Elapsed Time Program Time: 27:26:50 (hh:mm:ss) Elapsed Time