RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.fo7c86/RM_82431.WedNov290223322023 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: 1701253411 Database = /dev/shm/rModeler.fo7c86/GCF_030028045.1_mHipAmp2.hap2 - Sequences = 357 - Bases = 2538259262 - N50 = 171963845 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 224031161-240032215 | [ 2 ] 208030107-224031160 | [ ] 192029053-208030106 | [ 1 ] 176027999-192029052 | [ 1 ] 160026945-176027998 | [ 2 ] 144025891-160026944 | [ 3 ] 128024837-144025890 | [ 1 ] 112023784-128024837 | [ 2 ] 96022730-112023783 | [ 2 ] 80021676-96022729 | [ 1 ] 64020622-80021675 | [ 3 ] 48019568-64020621 | [ ] 32018514-48019567 | [ ] 16017460-32018513 | [ ] 16407-16017460 |************************************************** [ 339 ] Storage Throughput = excellent ( 1473.81 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40040910 bp ( 40039910 non ambiguous ) - Num Contigs Represented = 30 - Sequence extraction : 00:03:19 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:52 (hh:mm:ss) Elapsed Time Round Time: 00:31:35 (hh:mm:ss) Elapsed Time : 206 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9518 repeats masked totaling 2494024 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027344 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 10026944 bp After Masking: 7488663 bp Masked: 25.31 % -- Input Database Coverage: 10027344 bp out of 2538259262 bp ( 0.40 % ) Sampling Time: 00:01:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:19 (hh:mm:ss) Elapsed Time, 11517 HSPs Collected Number of families returned by RECON: 890 Round Time: 00:08:16 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34192 repeats masked totaling 9089799 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30013486 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 30012886 bp After Masking: 20756481 bp Masked: 30.84 % -- Input Database Coverage: 40040830 bp out of 2538259262 bp ( 1.58 % ) Sampling Time: 00:03:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:27:42 (hh:mm:ss) Elapsed Time, 45546 HSPs Collected Number of families returned by RECON: 2497 Round Time: 00:37:59 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 112701 repeats masked totaling 29752877 bp(s). - TE Masking time 00:01:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90029769 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 90028569 bp After Masking: 59751803 bp Masked: 33.63 % -- Input Database Coverage: 130070599 bp out of 2538259262 bp ( 5.12 % ) Sampling Time: 00:12:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 02:55:04 (hh:mm:ss) Elapsed Time, 139489 HSPs Collected Number of families returned by RECON: 9072 Round Time: 03:22:14 (hh:mm:ss) Elapsed Time : 202 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:22:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 387987 repeats masked totaling 101163483 bp(s). - TE Masking time 00:06:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270019068 bp Num Contigs Represented = 105 Non ambiguous bp: Initial: 270013868 bp After Masking: 167496581 bp Masked: 37.97 % -- Input Database Coverage: 400089667 bp out of 2538259262 bp ( 15.76 % ) Sampling Time: 00:39:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22899528 Comparison Time: 19:23:54 (hh:mm:ss) Elapsed Time, 218418 HSPs Collected Number of families returned by RECON: 34680 Round Time: 20:24:41 (hh:mm:ss) Elapsed Time : 370 families discovered. RepeatScout/RECON discovery complete: 864 families found Classification Time: 00:38:25 (hh:mm:ss) Elapsed Time Program Time: 25:43:10 (hh:mm:ss) Elapsed Time