RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Hcym3s/RM_30373.WedJan40327382023 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: 1672831656 Database = /dev/shm/rModeler.Hcym3s/GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w - Sequences = 276 - Bases = 1050511239 - N50 = 110406817 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 183160133-196242913 | [ 1 ] 170077353-183160132 | [ ] 156994574-170077353 | [ ] 143911794-156994573 | [ 1 ] 130829015-143911794 | [ ] 117746235-130829014 | [ ] 104663455-117746234 | [ 1 ] 91580676-104663455 | [ ] 78497896-91580675 | [ 2 ] 65415117-78497896 | [ ] 52332337-65415116 | [ 1 ] 39249557-52332336 | [ ] 26166778-39249557 | [ 3 ] 13083998-26166777 |* [ 7 ] 1219-13083998 |************************************************** [ 260 ] Storage Throughput = excellent ( 1147.48 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40119448 bp ( 40006061 non ambiguous ) - Num Contigs Represented = 59 - Sequence extraction : 00:02:03 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:10 (hh:mm:ss) Elapsed Time Round Time: 00:30:08 (hh:mm:ss) Elapsed Time : 145 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4411 repeats masked totaling 1216338 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10056492 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10009115 bp After Masking: 8679199 bp Masked: 13.29 % -- Input Database Coverage: 10056492 bp out of 1050511239 bp ( 0.96 % ) Sampling Time: 00:01:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:07:06 (hh:mm:ss) Elapsed Time, 785 HSPs Collected Number of families returned by RECON: 232 Round Time: 00:08:24 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11796 repeats masked totaling 3261563 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30102797 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 30036787 bp After Masking: 26309725 bp Masked: 12.41 % -- Input Database Coverage: 40159289 bp out of 1050511239 bp ( 3.82 % ) Sampling Time: 00:03:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:40:47 (hh:mm:ss) Elapsed Time, 64403 HSPs Collected Number of families returned by RECON: 1399 Round Time: 00:44:46 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 35287 repeats masked totaling 9196796 bp(s). - TE Masking time 00:01:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90345744 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 90026930 bp After Masking: 79728047 bp Masked: 11.44 % -- Input Database Coverage: 130505033 bp out of 1050511239 bp ( 12.42 % ) Sampling Time: 00:10:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2577585 Comparison Time: 04:58:17 (hh:mm:ss) Elapsed Time, 244291 HSPs Collected Number of families returned by RECON: 9093 Round Time: 05:12:26 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 114120 repeats masked totaling 29655523 bp(s). - TE Masking time 00:04:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271377304 bp Num Contigs Represented = 143 Non ambiguous bp: Initial: 270022739 bp After Masking: 235865446 bp Masked: 12.65 % -- Input Database Coverage: 401882337 bp out of 1050511239 bp ( 38.26 % ) Sampling Time: 00:35:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23273253 Comparison Time: 39:42:45 (hh:mm:ss) Elapsed Time, 255700 HSPs Collected Number of families returned by RECON: 60720 Round Time: 41:12:38 (hh:mm:ss) Elapsed Time : 233 families discovered. RepeatScout/RECON discovery complete: 446 families found Classification Time: 00:33:30 (hh:mm:ss) Elapsed Time Program Time: 48:21:52 (hh:mm:ss) Elapsed Time