RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.kkrqjr/RM_3893581.FriMar152054232024 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: 1710561262 Database = /dev/shm/rModeler.kkrqjr/GCA_036010785.1_bAmmMar1.pri - Sequences = 501 - Bases = 1397856043 - N50 = 77805107 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 150212288-160940846 | [ 1 ] 139483730-150212287 | [ ] 128755173-139483730 | [ ] 118026615-128755172 | [ 1 ] 107298058-118026615 | [ 1 ] 96569500-107298057 | [ 1 ] 85840943-96569500 | [ ] 75112385-85840942 | [ 2 ] 64383828-75112385 | [ 1 ] 53655270-64383827 | [ ] 42926713-53655270 | [ 2 ] 32198155-42926712 | [ 2 ] 21469598-32198155 | [ 4 ] 10741040-21469597 | [ 7 ] 12483-10741040 |************************************************** [ 479 ] Storage Throughput = excellent ( 1369.87 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40056395 bp ( 40034410 non ambiguous ) - Num Contigs Represented = 126 - Sequence extraction : 00:01:27 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:05 (hh:mm:ss) Elapsed Time Round Time: 00:33:10 (hh:mm:ss) Elapsed Time : 202 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4041 repeats masked totaling 1679102 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040363 bp Num Contigs Represented = 64 Non ambiguous bp: Initial: 10035697 bp After Masking: 7386675 bp Masked: 26.40 % -- Input Database Coverage: 10040363 bp out of 1397856043 bp ( 0.72 % ) Sampling Time: 00:02:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:57 (hh:mm:ss) Elapsed Time, 14123 HSPs Collected Number of families returned by RECON: 303 Round Time: 00:09:59 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11194 repeats masked totaling 4928276 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30055875 bp Num Contigs Represented = 110 Non ambiguous bp: Initial: 30038556 bp After Masking: 22034572 bp Masked: 26.65 % -- Input Database Coverage: 40096238 bp out of 1397856043 bp ( 2.87 % ) Sampling Time: 00:07:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:36:18 (hh:mm:ss) Elapsed Time, 17256 HSPs Collected Number of families returned by RECON: 1478 Round Time: 00:44:35 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 35824 repeats masked totaling 16336929 bp(s). - TE Masking time 00:01:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90227708 bp Num Contigs Represented = 191 Non ambiguous bp: Initial: 90036333 bp After Masking: 63708644 bp Masked: 29.24 % -- Input Database Coverage: 130323946 bp out of 1397856043 bp ( 9.32 % ) Sampling Time: 00:25:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2602621 Comparison Time: 03:05:15 (hh:mm:ss) Elapsed Time, 68511 HSPs Collected Number of families returned by RECON: 8119 Round Time: 03:42:10 (hh:mm:ss) Elapsed Time : 98 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:56:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 119789 repeats masked totaling 53407193 bp(s). - TE Masking time 00:07:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270488304 bp Num Contigs Represented = 268 Non ambiguous bp: Initial: 270032281 bp After Masking: 189684625 bp Masked: 29.75 % -- Input Database Coverage: 400812250 bp out of 1397856043 bp ( 28.67 % ) Sampling Time: 01:13:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23157415 Comparison Time: 22:59:21 (hh:mm:ss) Elapsed Time, 244277 HSPs Collected Number of families returned by RECON: 53750 Round Time: 25:07:24 (hh:mm:ss) Elapsed Time : 282 families discovered. RepeatScout/RECON discovery complete: 596 families found Classification Time: 00:53:32 (hh:mm:ss) Elapsed Time Program Time: 31:10:50 (hh:mm:ss) Elapsed Time