RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.tNwe8n/RM_574783.TueSep92354432025 Search Engine = rmblast 2.14.1+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.7, RepeatMasker 4.2.1, RepeatAfterMe 0.0.7 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1757487283 Database = /dev/shm/rModeler.tNwe8n/GCA_013146145.1_ASM1314614v1 - Sequences = 662 - Bases = 41454132 - N50 = 756493 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 2974030-3186432 | [ 1 ] 2761628-2974029 | [ ] 2549227-2761628 | [ 1 ] 2336825-2549226 | [ ] 2124423-2336824 | [ ] 1912022-2124423 | [ ] 1699620-1912021 | [ ] 1487218-1699619 | [ 1 ] 1274817-1487218 | [ 1 ] 1062415-1274816 | [ 6 ] 850013-1062414 | [ 1 ] 637612-850013 | [ 8 ] 425210-637611 |* [ 13 ] 212808-425209 |* [ 23 ] 407-212808 |************************************************** [ 607 ] Storage Throughput = excellent ( 1142.90 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40059629 bp ( 40032455 non ambiguous ) - Num Contigs Represented = 637 - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 89 raw families identified - RepeatScout: Running filtering stage.. 74 families remaining - RepeatScout: 00:01:16 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 69 families... 00:00:17 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 5 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time Round Time: 00:01:45 (hh:mm:ss) Elapsed Time : 64 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 550 repeats masked totaling 180926 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10013080 bp Num Contigs Represented = 198 Non ambiguous bp: Initial: 10006916 bp After Masking: 9811757 bp Masked: 1.95 % -- Input Database Coverage: 10013080 bp out of 41454132 bp ( 24.15 % ) Sampling Time: 00:00:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 71253 Comparison Time: 00:26:32 (hh:mm:ss) Elapsed Time, 1941 HSPs Collected Number of families returned by RECON: 800 Round Time: 03:53:55 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1734 repeats masked totaling 555116 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30046469 bp Num Contigs Represented = 502 Non ambiguous bp: Initial: 30025459 bp After Masking: 29426047 bp Masked: 2.00 % -- Input Database Coverage: 40059549 bp out of 41454132 bp ( 96.64 % ) Sampling Time: 00:01:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 668746 Comparison Time: 01:14:07 (hh:mm:ss) Elapsed Time, 19073 HSPs Collected Number of families returned by RECON: 4105 Round Time: 05:46:24 (hh:mm:ss) Elapsed Time : 11 families discovered. - Increasing sample size to include end piece now = 91441052 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 91441052 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 89 repeats masked totaling 27834 bp(s). - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 1394380 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 1393656 bp After Masking: 1362920 bp Masked: 2.21 % -- Input Database Coverage: 41453929 bp out of 41454132 bp ( 100.00 % ) Sampling Time: 00:00:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 1596 Comparison Time: 00:00:41 (hh:mm:ss) Elapsed Time, 30 HSPs Collected Number of families returned by RECON: 18 Round Time: 00:01:29 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 76 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.tNwe8n/RM_574783.TueSep92354432025 # Protein Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatPeps.lib # - 18011 proteins # Consensi Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatMasker.lib # - 26292 consensus sequences - Looking for simple/tandem and low complexity sequences.. - Looking for similarity to known repeat proteins.. - Looking for similarity to known repeat consensi.. Classification Time: 00:01:06 (hh:mm:ss) Elapsed Time Program Time: 09:44:39 (hh:mm:ss) Elapsed Time