RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.kvyiI3/RM_4143330.TueSep92207452025
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: 1757480864
Database = /dev/shm/rModeler.kvyiI3/GCA_011801205.1_ASM1180120v1 
  - Sequences = 14
  - Bases = 19089897
Storage Throughput = excellent ( 1085.73 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 19089775 bp ( 19089775 non ambiguous )
   - Num Contigs Represented = 14
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 46 raw families identified
   - RepeatScout: Running filtering stage.. 45 families remaining
   - RepeatScout: 00:00:52 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 44 families... 00:01:08 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 1 satellite(s), 4 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:02:07 (hh:mm:ss) Elapsed Time : 39 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 00:00:11 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       633 repeats masked totaling 437687 bp(s).
   - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10013379 bp
       Num Contigs Represented = 14
       Non ambiguous bp:
             Initial: 10013379 bp
             After Masking: 9564118 bp
             Masked: 4.49 % 
 -- Input Database Coverage: 10013379 bp out of 19089897 bp ( 52.45 % )
Sampling Time: 00:00:20 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 31626
Comparison Time: 00:05:21 (hh:mm:ss) Elapsed Time, 2112 HSPs Collected
Number of families returned by RECON: 613
Round Time: 00:05:48 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 39089897


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 39089897 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:10 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       893 repeats masked totaling 608793 bp(s).
   - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9076375 bp
       Num Contigs Represented = 14
       Non ambiguous bp:
             Initial: 9076375 bp
             After Masking: 8457199 bp
             Masked: 6.82 % 
 -- Input Database Coverage: 19089754 bp out of 19089897 bp ( 100.00 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 26565
Comparison Time: 00:04:35 (hh:mm:ss) Elapsed Time, 1582 HSPs Collected
Number of families returned by RECON: 512
Round Time: 00:05:04 (hh:mm:ss) Elapsed Time : 3 families discovered.

RepeatScout/RECON discovery complete: 43 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.kvyiI3/RM_4143330.TueSep92207452025
# 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: 00:00:38 (hh:mm:ss) Elapsed Time


Program Time: 00:13:37 (hh:mm:ss) Elapsed Time