RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.asn90V/RM_25114.ThuJan50451282023 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: 1672923087 Database = /dev/shm/rModeler.asn90V/GCF_015220235.1_mChoDid1.pri - Sequences = 146 - Bases = 3214702648 - N50 = 156022981 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 233953930-250664781 | [ 2 ] 217243080-233953930 | [ 1 ] 200532229-217243079 | [ ] 183821379-200532229 | [ 2 ] 167110529-183821379 | [ 1 ] 150399678-167110528 | [ 2 ] 133688828-150399678 | [ 2 ] 116977977-133688827 | [ 1 ] 100267127-116977977 | [ 1 ] 83556277-100267127 |** [ 5 ] 66845426-83556276 | [ 2 ] 50134576-66845426 |* [ 4 ] 33423725-50134575 | [ 1 ] 16712875-33423725 |* [ 4 ] 2025-16712875 |************************************************** [ 118 ] Storage Throughput = excellent ( 1392.34 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40656457 bp ( 40032913 non ambiguous ) - Num Contigs Represented = 46 - Sequence extraction : 00:03:49 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:51 (hh:mm:ss) Elapsed Time Round Time: 00:35:56 (hh:mm:ss) Elapsed Time : 213 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7997 repeats masked totaling 3599870 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10146464 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 10013124 bp After Masking: 6373787 bp Masked: 36.35 % -- Input Database Coverage: 10146464 bp out of 3214702648 bp ( 0.32 % ) Sampling Time: 00:01:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:05:45 (hh:mm:ss) Elapsed Time, 4843 HSPs Collected Number of families returned by RECON: 822 Round Time: 00:07:32 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26782 repeats masked totaling 12381214 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30509913 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 30019709 bp After Masking: 17544366 bp Masked: 41.56 % -- Input Database Coverage: 40656377 bp out of 3214702648 bp ( 1.26 % ) Sampling Time: 00:04:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 291466 Comparison Time: 00:24:35 (hh:mm:ss) Elapsed Time, 25988 HSPs Collected Number of families returned by RECON: 2307 Round Time: 00:29:46 (hh:mm:ss) Elapsed Time : 60 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 89135 repeats masked totaling 39805496 bp(s). - TE Masking time 00:01:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 92529650 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 90011468 bp After Masking: 49831969 bp Masked: 44.64 % -- Input Database Coverage: 133186027 bp out of 3214702648 bp ( 4.14 % ) Sampling Time: 00:12:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2685403 Comparison Time: 02:23:05 (hh:mm:ss) Elapsed Time, 71988 HSPs Collected Number of families returned by RECON: 7827 Round Time: 02:38:33 (hh:mm:ss) Elapsed Time : 134 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:22:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 294633 repeats masked totaling 123668667 bp(s). - TE Masking time 00:05:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 277798700 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 270016020 bp After Masking: 145194012 bp Masked: 46.23 % -- Input Database Coverage: 410984727 bp out of 3214702648 bp ( 12.78 % ) Sampling Time: 00:37:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24133878 Comparison Time: 18:26:23 (hh:mm:ss) Elapsed Time, 330573 HSPs Collected Number of families returned by RECON: 32909 Round Time: 19:37:23 (hh:mm:ss) Elapsed Time : 369 families discovered. RepeatScout/RECON discovery complete: 791 families found Classification Time: 00:53:28 (hh:mm:ss) Elapsed Time Program Time: 24:22:38 (hh:mm:ss) Elapsed Time