RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.niZSVG/RM_2125313.TueNov191117082024 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: 1732043828 Database = /scratch/tmp/rModeler.niZSVG/GCA_964094495.2_mMyoMys1.hap1.1 - Sequences = 526 - Bases = 2081199042 - N50 = 109453543 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 217139684-232649590 | [ 3 ] 201629778-217139684 | [ ] 186119872-201629778 | [ ] 170609966-186119872 | [ ] 155100060-170609966 | [ ] 139590154-155100060 | [ ] 124080248-139590154 | [ ] 108570342-124080248 | [ 3 ] 93060436-108570342 | [ 3 ] 77550530-93060436 | [ 3 ] 62040624-77550530 | [ 1 ] 46530718-62040624 | [ 5 ] 31020812-46530718 | [ 1 ] 15510906-31020812 | [ 3 ] 1000-15510906 |************************************************** [ 504 ] Storage Throughput = excellent ( 1474.94 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40013966 bp ( 40007966 non ambiguous ) - Num Contigs Represented = 47 - Sequence extraction : 00:01:22 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:04 (hh:mm:ss) Elapsed Time Round Time: 00:13:59 (hh:mm:ss) Elapsed Time : 353 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14935 repeats masked totaling 2865291 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10006593 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10004993 bp After Masking: 6885322 bp Masked: 31.18 % -- Input Database Coverage: 10006593 bp out of 2081199042 bp ( 0.48 % ) Sampling Time: 00:00:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:03:07 (hh:mm:ss) Elapsed Time, 5165 HSPs Collected Number of families returned by RECON: 888 Round Time: 00:04:00 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44066 repeats masked totaling 8156581 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30007370 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 30002970 bp After Masking: 20632374 bp Masked: 31.23 % -- Input Database Coverage: 40013963 bp out of 2081199042 bp ( 1.92 % ) Sampling Time: 00:02:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:14:14 (hh:mm:ss) Elapsed Time, 30407 HSPs Collected Number of families returned by RECON: 2623 Round Time: 00:16:57 (hh:mm:ss) Elapsed Time : 67 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 146196 repeats masked totaling 27384663 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90014950 bp Num Contigs Represented = 72 Non ambiguous bp: Initial: 90002350 bp After Masking: 59261275 bp Masked: 34.16 % -- Input Database Coverage: 130028913 bp out of 2081199042 bp ( 6.25 % ) Sampling Time: 00:05:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 01:32:00 (hh:mm:ss) Elapsed Time, 118940 HSPs Collected Number of families returned by RECON: 9531 Round Time: 01:41:09 (hh:mm:ss) Elapsed Time : 237 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 486931 repeats masked totaling 91174466 bp(s). - TE Masking time 00:03:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270065740 bp Num Contigs Represented = 179 Non ambiguous bp: Initial: 270025685 bp After Masking: 168290468 bp Masked: 37.68 % -- Input Database Coverage: 400094653 bp out of 2081199042 bp ( 19.22 % ) Sampling Time: 00:22:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23123400 Comparison Time: 09:33:27 (hh:mm:ss) Elapsed Time, 283202 HSPs Collected Number of families returned by RECON: 32974 Round Time: 10:07:44 (hh:mm:ss) Elapsed Time : 454 families discovered. RepeatScout/RECON discovery complete: 1120 families found Classification Time: 00:22:35 (hh:mm:ss) Elapsed Time Program Time: 12:46:24 (hh:mm:ss) Elapsed Time