RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.sPYpYO/RM_12460.MonNov271639252023 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: 1701131963 Database = /dev/shm/rModeler.sPYpYO/GCF_020745735.1_sHemOce1.pat.X.cur. - Sequences = 1962 - Bases = 3983466396 - N50 = 84986831 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 156391190-167561909 | [ 1 ] 145220472-156391190 | [ 2 ] 134049753-145220471 | [ 2 ] 122879035-134049753 | [ 2 ] 111708316-122879034 | [ 3 ] 100537598-111708316 | [ 2 ] 89366879-100537597 | [ 2 ] 78196161-89366879 | [ 4 ] 67025442-78196160 | [ 3 ] 55854724-67025442 | [ 8 ] 44684005-55854723 | [ 7 ] 33513287-44684005 | [ 5 ] 22342568-33513286 | [ 5 ] 11171850-22342568 | [ 4 ] 1132-11171850 |************************************************** [ 1912 ] Storage Throughput = excellent ( 1167.89 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40784710 bp ( 40000031 non ambiguous ) - Num Contigs Represented = 173 - Sequence extraction : 00:01:47 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:59 (hh:mm:ss) Elapsed Time Round Time: 00:29:10 (hh:mm:ss) Elapsed Time : 552 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22420 repeats masked totaling 5690422 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10231684 bp Num Contigs Represented = 86 Non ambiguous bp: Initial: 10014874 bp After Masking: 3929897 bp Masked: 60.76 % -- Input Database Coverage: 10231684 bp out of 3983466396 bp ( 0.26 % ) Sampling Time: 00:02:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33411 Comparison Time: 00:04:51 (hh:mm:ss) Elapsed Time, 5377 HSPs Collected Number of families returned by RECON: 836 Round Time: 00:07:27 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 66124 repeats masked totaling 16034406 bp(s). - TE Masking time 00:01:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30593026 bp Num Contigs Represented = 145 Non ambiguous bp: Initial: 30025157 bp After Masking: 12003343 bp Masked: 60.02 % -- Input Database Coverage: 40824710 bp out of 3983466396 bp ( 1.02 % ) Sampling Time: 00:08:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 301476 Comparison Time: 00:33:17 (hh:mm:ss) Elapsed Time, 47307 HSPs Collected Number of families returned by RECON: 2570 Round Time: 00:43:24 (hh:mm:ss) Elapsed Time : 61 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 210166 repeats masked totaling 50680949 bp(s). - TE Masking time 00:03:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91926491 bp Num Contigs Represented = 269 Non ambiguous bp: Initial: 90032421 bp After Masking: 34109546 bp Masked: 62.11 % -- Input Database Coverage: 132751201 bp out of 3983466396 bp ( 3.33 % ) Sampling Time: 00:27:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2703975 Comparison Time: 02:05:10 (hh:mm:ss) Elapsed Time, 267999 HSPs Collected Number of families returned by RECON: 7174 Round Time: 02:37:55 (hh:mm:ss) Elapsed Time : 252 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:56:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 681361 repeats masked totaling 163801331 bp(s). - TE Masking time 00:13:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 275041944 bp Num Contigs Represented = 578 Non ambiguous bp: Initial: 270026199 bp After Masking: 91007505 bp Masked: 66.30 % -- Input Database Coverage: 407793145 bp out of 3983466396 bp ( 10.24 % ) Sampling Time: 01:22:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24307878 Comparison Time: 15:03:33 (hh:mm:ss) Elapsed Time, 1432926 HSPs Collected Number of families returned by RECON: 20065 Round Time: 16:57:00 (hh:mm:ss) Elapsed Time : 684 families discovered. RepeatScout/RECON discovery complete: 1557 families found Classification Time: 01:20:40 (hh:mm:ss) Elapsed Time Program Time: 22:15:36 (hh:mm:ss) Elapsed Time