RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.KKEMYC/RM_3311965.SatJul191726192025 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: 1752971177 Database = /dev/shm/rModeler.KKEMYC/GCA_048593295.1_ASM4859329v1 - Sequences = 7 - Bases = 3272501082 Storage Throughput = excellent ( 1163.76 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40041489 bp ( 40038405 non ambiguous ) - Num Contigs Represented = 7 - Sequence extraction : 00:11:59 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:43 (hh:mm:ss) Elapsed Time Round Time: 00:46:05 (hh:mm:ss) Elapsed Time : 325 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:03:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15200 repeats masked totaling 3365536 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040015 bp Num Contigs Represented = 7 Non ambiguous bp: Initial: 10038605 bp After Masking: 6394777 bp Masked: 36.30 % -- Input Database Coverage: 10040015 bp out of 3272501082 bp ( 0.31 % ) Sampling Time: 00:03:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:38 (hh:mm:ss) Elapsed Time, 15853 HSPs Collected Number of families returned by RECON: 1492 Round Time: 00:10:07 (hh:mm:ss) Elapsed Time : 32 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:08:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 56317 repeats masked totaling 12007292 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30041316 bp Num Contigs Represented = 7 Non ambiguous bp: Initial: 30039642 bp After Masking: 17255746 bp Masked: 42.56 % -- Input Database Coverage: 40081331 bp out of 3272501082 bp ( 1.22 % ) Sampling Time: 00:12:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:28:45 (hh:mm:ss) Elapsed Time, 32257 HSPs Collected Number of families returned by RECON: 3309 Round Time: 00:42:18 (hh:mm:ss) Elapsed Time : 88 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:26:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 184580 repeats masked totaling 39400625 bp(s). - TE Masking time 00:02:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90040951 bp Num Contigs Represented = 7 Non ambiguous bp: Initial: 90033283 bp After Masking: 48271362 bp Masked: 46.38 % -- Input Database Coverage: 130122282 bp out of 3272501082 bp ( 3.98 % ) Sampling Time: 00:35:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 03:17:57 (hh:mm:ss) Elapsed Time, 83354 HSPs Collected Number of families returned by RECON: 10009 Round Time: 03:58:30 (hh:mm:ss) Elapsed Time : 179 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:19:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 598448 repeats masked totaling 125928096 bp(s). - TE Masking time 00:09:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270042679 bp Num Contigs Represented = 7 Non ambiguous bp: Initial: 270023121 bp After Masking: 136512463 bp Masked: 49.44 % -- Input Database Coverage: 400164961 bp out of 3272501082 bp ( 12.23 % ) Sampling Time: 01:51:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22784625 Comparison Time: 25:03:21 (hh:mm:ss) Elapsed Time, 347313 HSPs Collected Number of families returned by RECON: 37234 Round Time: 27:33:35 (hh:mm:ss) Elapsed Time : 480 families discovered. RepeatScout/RECON discovery complete: 1104 families found Classification Time: 00:37:24 (hh:mm:ss) Elapsed Time Program Time: 33:48:00 (hh:mm:ss) Elapsed Time