RepeatModeler Version 2.0.9
===========================
Using output directory = /dev/shm/rModeler.INETrb/RM_3674230.MonOct121729332026
Search Engine = rmblast 2.17.1+
Threads = 32
Dependencies: TRF 4.09, RECON /dev/shm/rModeler.INETrb/GCA_026743825.1_Candida_auris_PL1, RepeatScout 1.0.7, RepeatMasker 4.2.4, RepeatAfterMe 0.0.7
LTR Structural Analysis: Disabled [use -LTRStruct to enable]
Random Number Seed: 1791851372
Database = /dev/shm/rModeler.INETrb/GCA_026743825.1_Candida_auris_PL1 
  - Sequences = 781
  - Bases = 12235193
  - N50 = 41454
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  214935-230274 |                                                   [ 1 ]
  199597-214935 |                                                   [  ]
  184259-199597 |                                                   [  ]
  168921-184259 |                                                   [  ]
  153583-168921 |                                                   [  ]
  138245-153583 |                                                   [  ]
  122907-138245 |                                                   [ 1 ]
  107569-122907 |                                                   [ 1 ]
  92231-107569  |                                                   [ 8 ]
  76893-92231   |*                                                  [ 11 ]
  61555-76893   |*                                                  [ 17 ]
  46217-61555   |**                                                 [ 30 ]
  30879-46217   |*******                                            [ 76 ]
  15541-30879   |**********                                         [ 110 ]
  203-15541     |************************************************** [ 526 ]

Storage Throughput = excellent ( 1094.05 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 12235193 bp ( 12235193 non ambiguous )
   - Num Contigs Represented = 781
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 13, min = 10 )..
   - RepeatScout: Running RepeatScout.. : no families identified
   - RepeatScout: 00:00:23 (hh:mm:ss) Elapsed Time
NOTE: RepeatScout did not return any models.
Round Time: 00:00:25 (hh:mm:ss) Elapsed Time : 0 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
 -- Sample Stats:
       Sample Size 10014701 bp
       Num Contigs Represented = 645
       Non ambiguous bp:
             Initial: 10014701 bp
             After Masking: 10001628 bp
             Masked: 0.13 % 
 -- Input Database Coverage: 10014701 bp out of 12235193 bp ( 81.85 % )
Sampling Time: 00:00:13 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 272691
Comparison Time: 00:07:58 (hh:mm:ss) Elapsed Time, 3484 HSPs Collected
Number of families returned by RECON: 799
Round Time: 00:08:21 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 32235193


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 32235193 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       22 repeats masked totaling 2193 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 2220492 bp
       Num Contigs Represented = 164
       Non ambiguous bp:
             Initial: 2220492 bp
             After Masking: 2216091 bp
             Masked: 0.20 % 
 -- Input Database Coverage: 12235193 bp out of 12235193 bp ( 100.00 % )
Sampling Time: 00:00:05 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 13530
Comparison Time: 00:01:20 (hh:mm:ss) Elapsed Time, 107 HSPs Collected
Number of families returned by RECON: 63
Round Time: 00:01:25 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 2 families found


#
# RepeatClassifier
#
# Version 2.0.9
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.INETrb/RM_3674230.MonOct121729332026
# FamDB:
#   Database: Dfam
#    Version: 4.0
#       Date: 2026-05-22
# Protein Library: /hive/data/outside/RepeatModeler-2.0.9/Libraries/PROT-Dfam_4.0/repeatpeps.lib
#   - 18011 proteins
# Consensi Library: /hive/data/outside/RepeatModeler-2.0.9/Libraries/CONS-Dfam_4.0/reference.fa
#   - 30659 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: 00:00:18 (hh:mm:ss) Elapsed Time


Program Time: 00:10:29 (hh:mm:ss) Elapsed Time