nxf-scratch-dir c6a-s18:/scratch/local/57307408/nxf.oUvxI4nnl0
Executor: slurm  -  Time:null  -  Mem:10 GB  -  Queue: null
RepeatMasker -s -a -html -gff -dir RepeatMasker_Output  -pa 8 GCF_000005845.2_ASM584v2_genomic.fna
RepeatMasker version open-4.0.9
Search Engine: NCBI/RMBLAST [ 2.9.0+ ]
Master RepeatMasker Database: /apps/repeatmasker/4.0.9/share/RepeatMasker/Libraries/RepeatMaskerLib.embl ( Complete Database: CONS-Dfam_3.0 )



analyzing file GCF_000005845.2_ASM584v2_genomic.fna

Checking for E. coli insertion elements

Checking for E. coli insertion elements

Checking for E. coli insertion elements

Checking for E. coli insertion elements

Checking for E. coli insertion elements

Checking for E. coli insertion elements

Checking for E. coli insertion elements

Checking for E. coli insertion elements
identifying Simple Repeats in batch 2 of 80
The following E coli IS elements could not be confidently clipped out:
  IS186#ARTEFACT in NC_000913.3frag-1: 15493 - 15835
  IS186#ARTEFACT in NC_000913.3frag-1: 15880 - 15978
  IS186#ARTEFACT in NC_000913.3frag-1: 16089 - 16345
  IS186#ARTEFACT in NC_000913.3frag-1: 16521 - 16691
  IS1#ARTEFACT in NC_000913.3frag-1: 19820 - 20018
  IS1#ARTEFACT in NC_000913.3frag-1: 20144 - 20484
identifying Simple Repeats in batch 1 of 80
identifying Simple Repeats in batch 3 of 80
identifying Simple Repeats in batch 4 of 80
The following E coli IS elements could not be confidently clipped out:
  IS1#ARTEFACT in NC_000913.3frag-6: 683 - 881
  IS1#ARTEFACT in NC_000913.3frag-6: 1158 - 1347
  IS3#ARTEFACT in NC_000913.3frag-6: 25258 - 25617
  IS3#ARTEFACT in NC_000913.3frag-6: 26105 - 26307
identifying Simple Repeats in batch 6 of 80
identifying full-length ALUs in batch 2 of 80
The following E coli IS elements could not be confidently clipped out:
  IS1#ARTEFACT in NC_000913.3frag-5: 25952 - 26150
  IS1#ARTEFACT in NC_000913.3frag-5: 26276 - 26616
  IS30#ARTEFACT in NC_000913.3frag-5: 38665 - 38988
  IS30#ARTEFACT in NC_000913.3frag-5: 39691 - 39770
  IS5#ARTEFACT in NC_000913.3frag-5: 41990 - 43025
  IS1#ARTEFACT in NC_000913.3frag-5: 47207 - 47405
  IS1#ARTEFACT in NC_000913.3frag-5: 47682 - 47871
  IS30#ARTEFACT in NC_000913.3frag-5: 48041 - 48120
  IS1#ARTEFACT in NC_000913.3frag-5: 58678 - 58876
  IS1#ARTEFACT in NC_000913.3frag-5: 59153 - 59342
identifying Simple Repeats in batch 5 of 80
identifying full-length ALUs in batch 1 of 80
The following E coli IS elements could not be confidently clipped out:
  IS2#ARTEFACT in NC_000913.3frag-7: 33929 - 34572
  IS3#ARTEFACT in NC_000913.3frag-7: 43940 - 44142
  IS3#ARTEFACT in NC_000913.3frag-7: 44630 - 44992
identifying Simple Repeats in batch 7 of 80
identifying full-length ALUs in batch 3 of 80
identifying Simple Repeats in batch 8 of 80
identifying full-length ALUs in batch 4 of 80
identifying full-length ALUs in batch 6 of 80
identifying full-length ALUs in batch 5 of 80
identifying full-length ALUs in batch 7 of 80
identifying full-length ALUs in batch 8 of 80
identifying full-length interspersed repeats in batch 2 of 80
identifying full-length interspersed repeats in batch 3 of 80
identifying full-length interspersed repeats in batch 1 of 80
identifying full-length interspersed repeats in batch 4 of 80
identifying full-length interspersed repeats in batch 6 of 80
identifying full-length interspersed repeats in batch 5 of 80
identifying full-length interspersed repeats in batch 7 of 80
identifying full-length interspersed repeats in batch 8 of 80
identifying remaining ALUs in batch 2 of 80
identifying remaining ALUs in batch 3 of 80
identifying remaining ALUs in batch 1 of 80
identifying remaining ALUs in batch 6 of 80
identifying remaining ALUs in batch 5 of 80
identifying remaining ALUs in batch 4 of 80
identifying remaining ALUs in batch 7 of 80
identifying remaining ALUs in batch 8 of 80
identifying most interspersed repeats in batch 3 of 80
identifying most interspersed repeats in batch 2 of 80
identifying most interspersed repeats in batch 6 of 80
identifying most interspersed repeats in batch 1 of 80
identifying most interspersed repeats in batch 5 of 80
identifying most interspersed repeats in batch 7 of 80
identifying most interspersed repeats in batch 8 of 80
identifying most interspersed repeats in batch 4 of 80
identifying long interspersed repeats in batch 7 of 80
identifying long interspersed repeats in batch 6 of 80
identifying long interspersed repeats in batch 1 of 80
identifying long interspersed repeats in batch 2 of 80
identifying long interspersed repeats in batch 4 of 80
identifying long interspersed repeats in batch 5 of 80
identifying long interspersed repeats in batch 3 of 80
identifying long interspersed repeats in batch 8 of 80
identifying ancient repeats in batch 6 of 80
identifying ancient repeats in batch 7 of 80
identifying ancient repeats in batch 1 of 80
identifying ancient repeats in batch 2 of 80
identifying ancient repeats in batch 4 of 80
identifying ancient repeats in batch 3 of 80
identifying ancient repeats in batch 8 of 80
identifying ancient repeats in batch 5 of 80
identifying retrovirus-like sequences in batch 1 of 80
identifying retrovirus-like sequences in batch 4 of 80
identifying retrovirus-like sequences in batch 2 of 80
identifying retrovirus-like sequences in batch 7 of 80
identifying retrovirus-like sequences in batch 5 of 80
identifying retrovirus-like sequences in batch 6 of 80
identifying retrovirus-like sequences in batch 3 of 80
identifying retrovirus-like sequences in batch 8 of 80
identifying Simple Repeats in batch 1 of 80
identifying Simple Repeats in batch 4 of 80
identifying Simple Repeats in batch 7 of 80
identifying Simple Repeats in batch 2 of 80
identifying Simple Repeats in batch 5 of 80
identifying Simple Repeats in batch 6 of 80
identifying Simple Repeats in batch 8 of 80
identifying Simple Repeats in batch 3 of 80

Checking for E. coli insertion elements

Checking for E. coli insertion elements

Checking for E. coli insertion elements
identifying Simple Repeats in batch 9 of 80
The following E coli IS elements could not be confidently clipped out:
  IS3#ARTEFACT in NC_000913.3frag-10: 44826 - 45188
  IS3#ARTEFACT in NC_000913.3frag-10: 45676 - 45878
  IS5#ARTEFACT in NC_000913.3frag-10: 52651 - 53686
identifying Simple Repeats in batch 10 of 80

Checking for E. coli insertion elements
identifying full-length ALUs in batch 9 of 80
identifying full-length ALUs in batch 10 of 80
The following E coli IS elements could not be confidently clipped out:
  IS186#ARTEFACT in NC_000913.3frag-11: 28163 - 28505
  IS186#ARTEFACT in NC_000913.3frag-11: 28550 - 28648
  IS186#ARTEFACT in NC_000913.3frag-11: 28759 - 29015
  IS186#ARTEFACT in NC_000913.3frag-11: 29191 - 29361
identifying Simple Repeats in batch 11 of 80
identifying full-length ALUs in batch 11 of 80
identifying full-length interspersed repeats in batch 9 of 80
The following E coli IS elements could not be confidently clipped out:
  IS5#ARTEFACT in NC_000913.3frag-12: 49921 - 50956
identifying Simple Repeats in batch 12 of 80
identifying full-length interspersed repeats in batch 10 of 80
identifying full-length ALUs in batch 12 of 80
identifying full-length interspersed repeats in batch 11 of 80

Checking for E. coli insertion elements
identifying full-length interspersed repeats in batch 12 of 80
identifying Simple Repeats in batch 13 of 80
identifying remaining ALUs in batch 9 of 80
identifying remaining ALUs in batch 10 of 80
identifying full-length ALUs in batch 13 of 80

Checking for E. coli insertion elements
identifying remaining ALUs in batch 11 of 80
identifying full-length interspersed repeats in batch 13 of 80
identifying Simple Repeats in batch 14 of 80
identifying remaining ALUs in batch 12 of 80
identifying most interspersed repeats in batch 9 of 80

Checking for E. coli insertion elements
identifying full-length ALUs in batch 14 of 80
identifying most interspersed repeats in batch 10 of 80
identifying most interspersed repeats in batch 11 of 80
identifying Simple Repeats in batch 15 of 80
identifying full-length interspersed repeats in batch 14 of 80
identifying remaining ALUs in batch 13 of 80
identifying full-length ALUs in batch 15 of 80

Checking for E. coli insertion elements
identifying most interspersed repeats in batch 12 of 80
identifying full-length interspersed repeats in batch 15 of 80
identifying long interspersed repeats in batch 9 of 80
identifying Simple Repeats in batch 16 of 80
identifying long interspersed repeats in batch 10 of 80
identifying full-length ALUs in batch 16 of 80
identifying most interspersed repeats in batch 13 of 80
identifying remaining ALUs in batch 14 of 80
identifying long interspersed repeats in batch 11 of 80
identifying full-length interspersed repeats in batch 16 of 80
identifying remaining ALUs in batch 15 of 80
identifying ancient repeats in batch 9 of 80
identifying ancient repeats in batch 10 of 80
identifying long interspersed repeats in batch 12 of 80
identifying retrovirus-like sequences in batch 9 of 80
identifying most interspersed repeats in batch 14 of 80
identifying remaining ALUs in batch 16 of 80
identifying ancient repeats in batch 11 of 80
identifying long interspersed repeats in batch 13 of 80
identifying retrovirus-like sequences in batch 10 of 80
identifying most interspersed repeats in batch 15 of 80
identifying ancient repeats in batch 12 of 80
identifying Simple Repeats in batch 9 of 80
identifying retrovirus-like sequences in batch 11 of 80
identifying ancient repeats in batch 13 of 80
identifying Simple Repeats in batch 10 of 80
identifying most interspersed repeats in batch 16 of 80
identifying Simple Repeats in batch 11 of 80
identifying long interspersed repeats in batch 14 of 80
identifying retrovirus-like sequences in batch 12 of 80
identifying retrovirus-like sequences in batch 13 of 80
identifying long interspersed repeats in batch 15 of 80
identifying Simple Repeats in batch 12 of 80
identifying Simple Repeats in batch 13 of 80
identifying ancient repeats in batch 14 of 80
identifying ancient repeats in batch 15 of 80
identifying long interspersed repeats in batch 16 of 80
identifying retrovirus-like sequences in batch 14 of 80
identifying retrovirus-like sequences in batch 15 of 80
identifying ancient repeats in batch 16 of 80
identifying Simple Repeats in batch 15 of 80
identifying Simple Repeats in batch 14 of 80
identifying retrovirus-like sequences in batch 16 of 80
identifying Simple Repeats in batch 16 of 80

Checking for E. coli insertion elements
identifying Simple Repeats in batch 17 of 80

Checking for E. coli insertion elements
identifying full-length ALUs in batch 17 of 80

Checking for E. coli insertion elements
identifying Simple Repeats in batch 18 of 80
identifying full-length interspersed repeats in batch 17 of 80
identifying full-length ALUs in batch 18 of 80

Checking for E. coli insertion elements
The following E coli IS elements could not be confidently clipped out:
  IS1#ARTEFACT in NC_000913.3frag-19: 5965 - 6136
  IS1#ARTEFACT in NC_000913.3frag-19: 6413 - 6611
  IS3#ARTEFACT in NC_000913.3frag-19: 50536 - 50738
  IS3#ARTEFACT in NC_000913.3frag-19: 51226 - 51588
identifying Simple Repeats in batch 19 of 80
identifying full-length ALUs in batch 19 of 80
identifying Simple Repeats in batch 20 of 80
identifying full-length interspersed repeats in batch 18 of 80
identifying remaining ALUs in batch 17 of 80
identifying full-length ALUs in batch 20 of 80
identifying full-length interspersed repeats in batch 19 of 80
identifying full-length interspersed repeats in batch 20 of 80
identifying remaining ALUs in batch 18 of 80
identifying most interspersed repeats in batch 17 of 80
identifying remaining ALUs in batch 19 of 80
identifying remaining ALUs in batch 20 of 80

Checking for E. coli insertion elements

Checking for E. coli insertion elements
identifying most interspersed repeats in batch 18 of 80
identifying Simple Repeats in batch 22 of 80
identifying most interspersed repeats in batch 19 of 80
identifying Simple Repeats in batch 21 of 80
identifying full-length ALUs in batch 22 of 80

Checking for E. coli insertion elements
identifying long interspersed repeats in batch 17 of 80
identifying most interspersed repeats in batch 20 of 80

Checking for E. coli insertion elements
identifying full-length ALUs in batch 21 of 80
identifying full-length interspersed repeats in batch 22 of 80
The following E coli IS elements could not be confidently clipped out:
  IS5#ARTEFACT in NC_000913.3frag-23: 23753 - 24788
identifying Simple Repeats in batch 23 of 80
identifying full-length interspersed repeats in batch 21 of 80
identifying full-length ALUs in batch 23 of 80
identifying Simple Repeats in batch 24 of 80
identifying full-length ALUs in batch 24 of 80
identifying ancient repeats in batch 17 of 80
identifying long interspersed repeats in batch 19 of 80
identifying long interspersed repeats in batch 18 of 80
identifying remaining ALUs in batch 22 of 80
identifying full-length interspersed repeats in batch 23 of 80
identifying long interspersed repeats in batch 20 of 80
identifying full-length interspersed repeats in batch 24 of 80
identifying remaining ALUs in batch 21 of 80
identifying retrovirus-like sequences in batch 17 of 80
identifying ancient repeats in batch 19 of 80
identifying ancient repeats in batch 18 of 80
identifying most interspersed repeats in batch 22 of 80
identifying remaining ALUs in batch 23 of 80
identifying remaining ALUs in batch 24 of 80
identifying Simple Repeats in batch 17 of 80
identifying ancient repeats in batch 20 of 80
identifying most interspersed repeats in batch 21 of 80
identifying retrovirus-like sequences in batch 19 of 80
identifying retrovirus-like sequences in batch 18 of 80
identifying retrovirus-like sequences in batch 20 of 80
identifying most interspersed repeats in batch 24 of 80
identifying most interspersed repeats in batch 23 of 80
identifying Simple Repeats in batch 19 of 80
identifying long interspersed repeats in batch 22 of 80
identifying Simple Repeats in batch 18 of 80
identifying long interspersed repeats in batch 21 of 80
identifying Simple Repeats in batch 20 of 80
identifying ancient repeats in batch 22 of 80
identifying ancient repeats in batch 21 of 80
identifying long interspersed repeats in batch 23 of 80
identifying long interspersed repeats in batch 24 of 80
identifying retrovirus-like sequences in batch 22 of 80
identifying retrovirus-like sequences in batch 21 of 80
identifying ancient repeats in batch 23 of 80
identifying Simple Repeats in batch 22 of 80
identifying ancient repeats in batch 24 of 80
identifying Simple Repeats in batch 21 of 80
identifying retrovirus-like sequences in batch 23 of 80

Checking for E. coli insertion elements
identifying retrovirus-like sequences in batch 24 of 80
identifying Simple Repeats in batch 23 of 80
identifying Simple Repeats in batch 24 of 80
The following E coli IS elements could not be confidently clipped out:
  IS5#ARTEFACT in NC_000913.3frag-25: 4308 - 5343
  IS5#ARTEFACT in NC_000913.3frag-25: 35934 - 36550
identifying Simple Repeats in batch 25 of 80
identifying full-length ALUs in batch 25 of 80
identifying full-length interspersed repeats in batch 25 of 80

Checking for E. coli insertion elements
identifying remaining ALUs in batch 25 of 80
The following E coli IS elements could not be confidently clipped out:
  IS2#ARTEFACT in NC_000913.3frag-26: 18083 - 18726
  IS30#ARTEFACT in NC_000913.3frag-26: 19525 - 19848
  IS30#ARTEFACT in NC_000913.3frag-26: 20551 - 20630
identifying Simple Repeats in batch 26 of 80

Checking for E. coli insertion elements
identifying full-length ALUs in batch 26 of 80
identifying Simple Repeats in batch 27 of 80
identifying full-length interspersed repeats in batch 26 of 80
identifying most interspersed repeats in batch 25 of 80
identifying full-length ALUs in batch 27 of 80
identifying full-length interspersed repeats in batch 27 of 80

Checking for E. coli insertion elements
identifying remaining ALUs in batch 26 of 80
identifying long interspersed repeats in batch 25 of 80
identifying Simple Repeats in batch 28 of 80
identifying remaining ALUs in batch 27 of 80
identifying full-length ALUs in batch 28 of 80
identifying ancient repeats in batch 25 of 80

Checking for E. coli insertion elements
identifying full-length interspersed repeats in batch 28 of 80
identifying most interspersed repeats in batch 26 of 80
The following E coli IS elements could not be confidently clipped out:
  IS2#ARTEFACT in NC_000913.3frag-29: 26997 - 27640
identifying Simple Repeats in batch 29 of 80

Checking for E. coli insertion elements
identifying retrovirus-like sequences in batch 25 of 80
identifying full-length ALUs in batch 29 of 80
identifying most interspersed repeats in batch 27 of 80

Checking for E. coli insertion elements
identifying Simple Repeats in batch 25 of 80
identifying Simple Repeats in batch 30 of 80
identifying full-length interspersed repeats in batch 29 of 80
identifying remaining ALUs in batch 28 of 80
identifying full-length ALUs in batch 30 of 80
identifying long interspersed repeats in batch 26 of 80
identifying Simple Repeats in batch 31 of 80
identifying full-length ALUs in batch 31 of 80
identifying long interspersed repeats in batch 27 of 80
identifying full-length interspersed repeats in batch 30 of 80
identifying remaining ALUs in batch 29 of 80
identifying full-length interspersed repeats in batch 31 of 80

Checking for E. coli insertion elements
identifying ancient repeats in batch 26 of 80
identifying most interspersed repeats in batch 28 of 80
identifying ancient repeats in batch 27 of 80
identifying Simple Repeats in batch 32 of 80
identifying remaining ALUs in batch 30 of 80
identifying retrovirus-like sequences in batch 26 of 80
identifying full-length ALUs in batch 32 of 80
identifying remaining ALUs in batch 31 of 80
identifying most interspersed repeats in batch 29 of 80
identifying retrovirus-like sequences in batch 27 of 80
identifying Simple Repeats in batch 26 of 80
identifying full-length interspersed repeats in batch 32 of 80
identifying most interspersed repeats in batch 30 of 80
identifying long interspersed repeats in batch 28 of 80
identifying most interspersed repeats in batch 31 of 80
identifying Simple Repeats in batch 27 of 80
identifying long interspersed repeats in batch 29 of 80
identifying remaining ALUs in batch 32 of 80
identifying long interspersed repeats in batch 30 of 80
identifying ancient repeats in batch 28 of 80
identifying long interspersed repeats in batch 31 of 80
identifying ancient repeats in batch 29 of 80
identifying retrovirus-like sequences in batch 28 of 80
identifying ancient repeats in batch 30 of 80
identifying ancient repeats in batch 31 of 80
identifying most interspersed repeats in batch 32 of 80

Checking for E. coli insertion elements
identifying retrovirus-like sequences in batch 29 of 80
identifying Simple Repeats in batch 28 of 80
identifying Simple Repeats in batch 33 of 80
identifying Simple Repeats in batch 29 of 80
identifying full-length ALUs in batch 33 of 80
identifying retrovirus-like sequences in batch 30 of 80
identifying retrovirus-like sequences in batch 31 of 80

Checking for E. coli insertion elements
identifying long interspersed repeats in batch 32 of 80
identifying Simple Repeats in batch 30 of 80
identifying Simple Repeats in batch 31 of 80
identifying full-length interspersed repeats in batch 33 of 80
identifying Simple Repeats in batch 34 of 80
identifying full-length ALUs in batch 34 of 80
identifying ancient repeats in batch 32 of 80
identifying full-length interspersed repeats in batch 34 of 80
identifying remaining ALUs in batch 33 of 80
identifying retrovirus-like sequences in batch 32 of 80
identifying remaining ALUs in batch 34 of 80

Checking for E. coli insertion elements
identifying Simple Repeats in batch 32 of 80
identifying most interspersed repeats in batch 33 of 80
The following E coli IS elements could not be confidently clipped out:
  IS1#ARTEFACT in NC_000913.3frag-35: 6697 - 6895
  IS1#ARTEFACT in NC_000913.3frag-35: 7021 - 7361
identifying Simple Repeats in batch 35 of 80
identifying full-length ALUs in batch 35 of 80
identifying most interspersed repeats in batch 34 of 80
identifying long interspersed repeats in batch 33 of 80

Checking for E. coli insertion elements
identifying full-length interspersed repeats in batch 35 of 80

Checking for E. coli insertion elements
The following E coli IS elements could not be confidently clipped out:
  IS5#ARTEFACT in NC_000913.3frag-36: 36358 - 37440
  IS2#ARTEFACT in NC_000913.3frag-36: 39164 - 39807
identifying Simple Repeats in batch 36 of 80
The following E coli IS elements could not be confidently clipped out:
  IS5#ARTEFACT in NC_000913.3frag-37: 13944 - 14979
identifying Simple Repeats in batch 37 of 80
identifying long interspersed repeats in batch 34 of 80
identifying full-length ALUs in batch 36 of 80
identifying full-length ALUs in batch 37 of 80
identifying ancient repeats in batch 33 of 80
identifying remaining ALUs in batch 35 of 80
identifying full-length interspersed repeats in batch 36 of 80
identifying full-length interspersed repeats in batch 37 of 80
identifying ancient repeats in batch 34 of 80
identifying retrovirus-like sequences in batch 33 of 80
identifying remaining ALUs in batch 37 of 80

Checking for E. coli insertion elements
identifying most interspersed repeats in batch 35 of 80
identifying Simple Repeats in batch 33 of 80
identifying remaining ALUs in batch 36 of 80
identifying retrovirus-like sequences in batch 34 of 80
The following E coli IS elements could not be confidently clipped out:
  IS3#ARTEFACT in NC_000913.3frag-38: 24360 - 24722
  IS3#ARTEFACT in NC_000913.3frag-38: 25210 - 25412
identifying Simple Repeats in batch 38 of 80
identifying most interspersed repeats in batch 37 of 80
identifying Simple Repeats in batch 34 of 80
identifying full-length ALUs in batch 38 of 80

Checking for E. coli insertion elements
identifying most interspersed repeats in batch 36 of 80
identifying long interspersed repeats in batch 35 of 80
identifying full-length interspersed repeats in batch 38 of 80
identifying Simple Repeats in batch 39 of 80
identifying long interspersed repeats in batch 37 of 80
identifying full-length ALUs in batch 39 of 80

Checking for E. coli insertion elements
identifying full-length interspersed repeats in batch 39 of 80
identifying ancient repeats in batch 35 of 80
identifying long interspersed repeats in batch 36 of 80
The following E coli IS elements could not be confidently clipped out:
  IS5#ARTEFACT in NC_000913.3frag-40: 27129 - 28164
identifying Simple Repeats in batch 40 of 80
identifying remaining ALUs in batch 38 of 80
identifying ancient repeats in batch 37 of 80
identifying full-length ALUs in batch 40 of 80
identifying retrovirus-like sequences in batch 35 of 80
identifying remaining ALUs in batch 39 of 80
identifying full-length interspersed repeats in batch 40 of 80
identifying retrovirus-like sequences in batch 37 of 80
identifying ancient repeats in batch 36 of 80
identifying Simple Repeats in batch 35 of 80
identifying most interspersed repeats in batch 38 of 80
identifying Simple Repeats in batch 37 of 80
identifying most interspersed repeats in batch 39 of 80
identifying remaining ALUs in batch 40 of 80
identifying retrovirus-like sequences in batch 36 of 80
identifying long interspersed repeats in batch 38 of 80
identifying Simple Repeats in batch 36 of 80
identifying long interspersed repeats in batch 39 of 80
identifying ancient repeats in batch 38 of 80
identifying most interspersed repeats in batch 40 of 80
identifying ancient repeats in batch 39 of 80
identifying retrovirus-like sequences in batch 38 of 80
identifying Simple Repeats in batch 38 of 80

Checking for E. coli insertion elements
identifying retrovirus-like sequences in batch 39 of 80
identifying long interspersed repeats in batch 40 of 80

Checking for E. coli insertion elements
identifying Simple Repeats in batch 41 of 80
identifying Simple Repeats in batch 39 of 80
identifying full-length ALUs in batch 41 of 80
identifying Simple Repeats in batch 42 of 80
identifying full-length interspersed repeats in batch 41 of 80

Checking for E. coli insertion elements
identifying full-length ALUs in batch 42 of 80
identifying ancient repeats in batch 40 of 80
identifying full-length interspersed repeats in batch 42 of 80
identifying Simple Repeats in batch 43 of 80
identifying retrovirus-like sequences in batch 40 of 80
identifying full-length ALUs in batch 43 of 80
identifying remaining ALUs in batch 41 of 80
identifying Simple Repeats in batch 40 of 80
identifying full-length interspersed repeats in batch 43 of 80
identifying remaining ALUs in batch 42 of 80

Checking for E. coli insertion elements
identifying most interspersed repeats in batch 41 of 80
The following E coli IS elements could not be confidently clipped out:
  IS186#ARTEFACT in NC_000913.3frag-44: 20594 - 20936
  IS186#ARTEFACT in NC_000913.3frag-44: 20981 - 21079
  IS186#ARTEFACT in NC_000913.3frag-44: 21190 - 21446
  IS186#ARTEFACT in NC_000913.3frag-44: 21622 - 21792
identifying Simple Repeats in batch 44 of 80
identifying remaining ALUs in batch 43 of 80

Checking for E. coli insertion elements
identifying full-length ALUs in batch 44 of 80
identifying most interspersed repeats in batch 42 of 80
identifying full-length interspersed repeats in batch 44 of 80
identifying long interspersed repeats in batch 41 of 80
identifying Simple Repeats in batch 45 of 80
identifying most interspersed repeats in batch 43 of 80
identifying long interspersed repeats in batch 42 of 80
identifying full-length ALUs in batch 45 of 80
identifying remaining ALUs in batch 44 of 80

Checking for E. coli insertion elements
identifying ancient repeats in batch 41 of 80
identifying ancient repeats in batch 42 of 80
identifying full-length interspersed repeats in batch 45 of 80
identifying long interspersed repeats in batch 43 of 80
identifying Simple Repeats in batch 46 of 80
identifying most interspersed repeats in batch 44 of 80
identifying full-length ALUs in batch 46 of 80
identifying retrovirus-like sequences in batch 41 of 80
identifying retrovirus-like sequences in batch 42 of 80
identifying remaining ALUs in batch 45 of 80
identifying ancient repeats in batch 43 of 80
identifying full-length interspersed repeats in batch 46 of 80
identifying Simple Repeats in batch 41 of 80
identifying Simple Repeats in batch 42 of 80

Checking for E. coli insertion elements
identifying long interspersed repeats in batch 44 of 80
identifying retrovirus-like sequences in batch 43 of 80
identifying remaining ALUs in batch 46 of 80
identifying most interspersed repeats in batch 45 of 80
identifying Simple Repeats in batch 47 of 80
identifying full-length ALUs in batch 47 of 80
identifying Simple Repeats in batch 43 of 80
identifying full-length interspersed repeats in batch 47 of 80

Checking for E. coli insertion elements
identifying ancient repeats in batch 44 of 80
identifying most interspersed repeats in batch 46 of 80
identifying Simple Repeats in batch 48 of 80
identifying retrovirus-like sequences in batch 44 of 80
identifying full-length ALUs in batch 48 of 80
identifying long interspersed repeats in batch 45 of 80
identifying remaining ALUs in batch 47 of 80
identifying full-length interspersed repeats in batch 48 of 80
identifying long interspersed repeats in batch 46 of 80
identifying Simple Repeats in batch 44 of 80
identifying ancient repeats in batch 45 of 80
identifying remaining ALUs in batch 48 of 80
identifying most interspersed repeats in batch 47 of 80
identifying ancient repeats in batch 46 of 80
identifying retrovirus-like sequences in batch 45 of 80
identifying retrovirus-like sequences in batch 46 of 80

Checking for E. coli insertion elements
identifying most interspersed repeats in batch 48 of 80

Checking for E. coli insertion elements
identifying long interspersed repeats in batch 47 of 80
identifying Simple Repeats in batch 49 of 80
identifying Simple Repeats in batch 46 of 80
identifying Simple Repeats in batch 45 of 80
identifying Simple Repeats in batch 50 of 80
identifying full-length ALUs in batch 49 of 80
identifying full-length ALUs in batch 50 of 80
identifying long interspersed repeats in batch 48 of 80
identifying ancient repeats in batch 47 of 80
identifying full-length interspersed repeats in batch 50 of 80
identifying full-length interspersed repeats in batch 49 of 80
identifying retrovirus-like sequences in batch 47 of 80
identifying ancient repeats in batch 48 of 80

Checking for E. coli insertion elements
identifying Simple Repeats in batch 47 of 80
identifying remaining ALUs in batch 50 of 80
identifying Simple Repeats in batch 51 of 80
identifying full-length ALUs in batch 51 of 80
identifying retrovirus-like sequences in batch 48 of 80
identifying remaining ALUs in batch 49 of 80
identifying full-length interspersed repeats in batch 51 of 80
identifying Simple Repeats in batch 48 of 80
identifying most interspersed repeats in batch 50 of 80
identifying most interspersed repeats in batch 49 of 80
identifying long interspersed repeats in batch 50 of 80
identifying remaining ALUs in batch 51 of 80

Checking for E. coli insertion elements

Checking for E. coli insertion elements
identifying ancient repeats in batch 50 of 80
identifying long interspersed repeats in batch 49 of 80
The following E coli IS elements could not be confidently clipped out:
  IS2#ARTEFACT in NC_000913.3frag-52: 38664 - 39307
identifying Simple Repeats in batch 52 of 80
identifying Simple Repeats in batch 53 of 80
identifying full-length ALUs in batch 52 of 80
identifying full-length ALUs in batch 53 of 80
identifying retrovirus-like sequences in batch 50 of 80
identifying most interspersed repeats in batch 51 of 80
identifying full-length interspersed repeats in batch 52 of 80
identifying full-length interspersed repeats in batch 53 of 80
identifying ancient repeats in batch 49 of 80
identifying Simple Repeats in batch 50 of 80

Checking for E. coli insertion elements
identifying retrovirus-like sequences in batch 49 of 80
identifying remaining ALUs in batch 53 of 80
The following E coli IS elements could not be confidently clipped out:
  IS5#ARTEFACT in NC_000913.3frag-54: 56555 - 57590
identifying Simple Repeats in batch 54 of 80
identifying remaining ALUs in batch 52 of 80
identifying Simple Repeats in batch 49 of 80
identifying full-length ALUs in batch 54 of 80
identifying long interspersed repeats in batch 51 of 80
identifying full-length interspersed repeats in batch 54 of 80
identifying most interspersed repeats in batch 53 of 80
identifying most interspersed repeats in batch 52 of 80
identifying ancient repeats in batch 51 of 80
identifying remaining ALUs in batch 54 of 80
identifying retrovirus-like sequences in batch 51 of 80

Checking for E. coli insertion elements

Checking for E. coli insertion elements
identifying long interspersed repeats in batch 53 of 80
The following E coli IS elements could not be confidently clipped out:
  IS2#ARTEFACT in NC_000913.3frag-55: 55005 - 55648
identifying Simple Repeats in batch 55 of 80
identifying Simple Repeats in batch 56 of 80
identifying long interspersed repeats in batch 52 of 80
identifying full-length ALUs in batch 55 of 80
identifying full-length ALUs in batch 56 of 80
identifying Simple Repeats in batch 51 of 80
identifying most interspersed repeats in batch 54 of 80
identifying full-length interspersed repeats in batch 55 of 80
identifying ancient repeats in batch 53 of 80
identifying full-length interspersed repeats in batch 56 of 80
identifying ancient repeats in batch 52 of 80
identifying retrovirus-like sequences in batch 53 of 80
identifying remaining ALUs in batch 55 of 80
identifying long interspersed repeats in batch 54 of 80
identifying retrovirus-like sequences in batch 52 of 80

Checking for E. coli insertion elements
identifying Simple Repeats in batch 53 of 80
identifying remaining ALUs in batch 56 of 80
identifying Simple Repeats in batch 57 of 80
identifying most interspersed repeats in batch 55 of 80
identifying Simple Repeats in batch 52 of 80
identifying full-length ALUs in batch 57 of 80
identifying ancient repeats in batch 54 of 80
identifying full-length interspersed repeats in batch 57 of 80
identifying most interspersed repeats in batch 56 of 80
identifying retrovirus-like sequences in batch 54 of 80
identifying long interspersed repeats in batch 55 of 80

Checking for E. coli insertion elements
identifying Simple Repeats in batch 54 of 80
identifying long interspersed repeats in batch 56 of 80
identifying ancient repeats in batch 55 of 80
identifying remaining ALUs in batch 57 of 80
The following E coli IS elements could not be confidently clipped out:
  IS5#ARTEFACT in NC_000913.3frag-58: 59865 - 59988
identifying Simple Repeats in batch 58 of 80
identifying full-length ALUs in batch 58 of 80
identifying retrovirus-like sequences in batch 55 of 80
identifying ancient repeats in batch 56 of 80
identifying full-length interspersed repeats in batch 58 of 80
identifying Simple Repeats in batch 55 of 80
identifying most interspersed repeats in batch 57 of 80
identifying retrovirus-like sequences in batch 56 of 80

Checking for E. coli insertion elements
identifying remaining ALUs in batch 58 of 80
identifying Simple Repeats in batch 56 of 80
The following E coli IS elements could not be confidently clipped out:
  IS5#ARTEFACT in NC_000913.3frag-59: 1861 - 2896
identifying Simple Repeats in batch 59 of 80
identifying full-length ALUs in batch 59 of 80
identifying most interspersed repeats in batch 58 of 80
identifying long interspersed repeats in batch 57 of 80
identifying full-length interspersed repeats in batch 59 of 80

Checking for E. coli insertion elements
identifying ancient repeats in batch 57 of 80
identifying long interspersed repeats in batch 58 of 80

Checking for E. coli insertion elements
identifying Simple Repeats in batch 60 of 80
identifying remaining ALUs in batch 59 of 80

Checking for E. coli insertion elements
identifying Simple Repeats in batch 61 of 80
identifying retrovirus-like sequences in batch 57 of 80
identifying full-length ALUs in batch 60 of 80
identifying full-length ALUs in batch 61 of 80
identifying ancient repeats in batch 58 of 80
The following E coli IS elements could not be confidently clipped out:
  IS1#ARTEFACT in NC_000913.3frag-62: 45812 - 46152
  IS1#ARTEFACT in NC_000913.3frag-62: 46278 - 46476
identifying Simple Repeats in batch 62 of 80
identifying Simple Repeats in batch 57 of 80
identifying full-length interspersed repeats in batch 60 of 80
identifying full-length ALUs in batch 62 of 80
identifying full-length interspersed repeats in batch 61 of 80
identifying most interspersed repeats in batch 59 of 80
identifying retrovirus-like sequences in batch 58 of 80
identifying full-length interspersed repeats in batch 62 of 80
identifying Simple Repeats in batch 58 of 80
identifying remaining ALUs in batch 60 of 80
identifying long interspersed repeats in batch 59 of 80
identifying remaining ALUs in batch 61 of 80
identifying remaining ALUs in batch 62 of 80
identifying most interspersed repeats in batch 60 of 80
identifying ancient repeats in batch 59 of 80
identifying most interspersed repeats in batch 61 of 80

Checking for E. coli insertion elements
identifying most interspersed repeats in batch 62 of 80
identifying retrovirus-like sequences in batch 59 of 80
identifying long interspersed repeats in batch 60 of 80
The following E coli IS elements could not be confidently clipped out:
  IS5#ARTEFACT in NC_000913.3frag-63: 56361 - 57396
identifying Simple Repeats in batch 63 of 80
identifying long interspersed repeats in batch 61 of 80
identifying full-length ALUs in batch 63 of 80

Checking for E. coli insertion elements
identifying Simple Repeats in batch 59 of 80
identifying long interspersed repeats in batch 62 of 80
identifying Simple Repeats in batch 64 of 80

Checking for E. coli insertion elements
identifying full-length interspersed repeats in batch 63 of 80
identifying ancient repeats in batch 60 of 80
identifying full-length ALUs in batch 64 of 80
The following E coli IS elements could not be confidently clipped out:
  IS150#ARTEFACT in NC_000913.3frag-65: 9610 - 9900
identifying Simple Repeats in batch 65 of 80
identifying ancient repeats in batch 62 of 80
identifying ancient repeats in batch 61 of 80
identifying full-length ALUs in batch 65 of 80
identifying full-length interspersed repeats in batch 64 of 80
identifying retrovirus-like sequences in batch 60 of 80
identifying remaining ALUs in batch 63 of 80
identifying full-length interspersed repeats in batch 65 of 80
identifying retrovirus-like sequences in batch 62 of 80
identifying Simple Repeats in batch 60 of 80
identifying retrovirus-like sequences in batch 61 of 80
identifying remaining ALUs in batch 64 of 80
identifying Simple Repeats in batch 62 of 80
identifying most interspersed repeats in batch 63 of 80
identifying Simple Repeats in batch 61 of 80
identifying remaining ALUs in batch 65 of 80

Checking for E. coli insertion elements
identifying most interspersed repeats in batch 64 of 80
identifying Simple Repeats in batch 66 of 80
identifying long interspersed repeats in batch 63 of 80
identifying full-length ALUs in batch 66 of 80
identifying most interspersed repeats in batch 65 of 80
identifying long interspersed repeats in batch 64 of 80
identifying full-length interspersed repeats in batch 66 of 80
identifying ancient repeats in batch 63 of 80
identifying long interspersed repeats in batch 65 of 80

Checking for E. coli insertion elements
identifying remaining ALUs in batch 66 of 80
identifying retrovirus-like sequences in batch 63 of 80
identifying ancient repeats in batch 64 of 80
identifying Simple Repeats in batch 67 of 80
identifying Simple Repeats in batch 63 of 80
identifying full-length ALUs in batch 67 of 80
identifying ancient repeats in batch 65 of 80

Checking for E. coli insertion elements
identifying full-length interspersed repeats in batch 67 of 80
identifying most interspersed repeats in batch 66 of 80
identifying retrovirus-like sequences in batch 64 of 80
identifying Simple Repeats in batch 68 of 80
identifying Simple Repeats in batch 64 of 80
identifying full-length ALUs in batch 68 of 80
identifying retrovirus-like sequences in batch 65 of 80
identifying remaining ALUs in batch 67 of 80
identifying Simple Repeats in batch 65 of 80
identifying full-length interspersed repeats in batch 68 of 80
identifying long interspersed repeats in batch 66 of 80
identifying most interspersed repeats in batch 67 of 80

Checking for E. coli insertion elements
identifying remaining ALUs in batch 68 of 80

Checking for E. coli insertion elements
identifying ancient repeats in batch 66 of 80
identifying Simple Repeats in batch 70 of 80
identifying Simple Repeats in batch 69 of 80
identifying full-length ALUs in batch 70 of 80
identifying retrovirus-like sequences in batch 66 of 80
identifying long interspersed repeats in batch 67 of 80
identifying full-length ALUs in batch 69 of 80
identifying most interspersed repeats in batch 68 of 80
identifying full-length interspersed repeats in batch 70 of 80
identifying Simple Repeats in batch 66 of 80
identifying full-length interspersed repeats in batch 69 of 80
identifying ancient repeats in batch 67 of 80
identifying long interspersed repeats in batch 68 of 80
identifying remaining ALUs in batch 70 of 80

Checking for E. coli insertion elements
identifying retrovirus-like sequences in batch 67 of 80
identifying remaining ALUs in batch 69 of 80
identifying ancient repeats in batch 68 of 80
identifying Simple Repeats in batch 71 of 80
identifying Simple Repeats in batch 67 of 80
identifying full-length ALUs in batch 71 of 80
identifying most interspersed repeats in batch 70 of 80
identifying most interspersed repeats in batch 69 of 80
identifying retrovirus-like sequences in batch 68 of 80
identifying full-length interspersed repeats in batch 71 of 80

Checking for E. coli insertion elements
identifying long interspersed repeats in batch 70 of 80
identifying Simple Repeats in batch 72 of 80
identifying Simple Repeats in batch 68 of 80
identifying full-length ALUs in batch 72 of 80
identifying long interspersed repeats in batch 69 of 80
identifying remaining ALUs in batch 71 of 80
identifying ancient repeats in batch 70 of 80
identifying full-length interspersed repeats in batch 72 of 80
identifying ancient repeats in batch 69 of 80

Checking for E. coli insertion elements
identifying most interspersed repeats in batch 71 of 80
identifying retrovirus-like sequences in batch 70 of 80
identifying remaining ALUs in batch 72 of 80
identifying Simple Repeats in batch 73 of 80
identifying retrovirus-like sequences in batch 69 of 80
identifying Simple Repeats in batch 70 of 80
identifying full-length ALUs in batch 73 of 80
identifying long interspersed repeats in batch 71 of 80

Checking for E. coli insertion elements
identifying Simple Repeats in batch 69 of 80
identifying full-length interspersed repeats in batch 73 of 80
identifying most interspersed repeats in batch 72 of 80
identifying Simple Repeats in batch 74 of 80

Checking for E. coli insertion elements
identifying full-length ALUs in batch 74 of 80
identifying ancient repeats in batch 71 of 80
identifying Simple Repeats in batch 75 of 80
identifying remaining ALUs in batch 73 of 80
identifying full-length interspersed repeats in batch 74 of 80
identifying full-length ALUs in batch 75 of 80
identifying long interspersed repeats in batch 72 of 80
identifying retrovirus-like sequences in batch 71 of 80
identifying full-length interspersed repeats in batch 75 of 80
identifying Simple Repeats in batch 71 of 80
identifying most interspersed repeats in batch 73 of 80
identifying remaining ALUs in batch 74 of 80
identifying ancient repeats in batch 72 of 80
identifying remaining ALUs in batch 75 of 80
identifying most interspersed repeats in batch 74 of 80
identifying retrovirus-like sequences in batch 72 of 80
identifying long interspersed repeats in batch 73 of 80

Checking for E. coli insertion elements

Checking for E. coli insertion elements
identifying most interspersed repeats in batch 75 of 80
identifying Simple Repeats in batch 72 of 80
identifying Simple Repeats in batch 76 of 80
identifying Simple Repeats in batch 77 of 80
identifying full-length ALUs in batch 76 of 80
identifying long interspersed repeats in batch 74 of 80
identifying full-length ALUs in batch 77 of 80
identifying ancient repeats in batch 73 of 80
identifying full-length interspersed repeats in batch 77 of 80
identifying full-length interspersed repeats in batch 76 of 80
identifying ancient repeats in batch 74 of 80
identifying long interspersed repeats in batch 75 of 80
identifying retrovirus-like sequences in batch 73 of 80
identifying retrovirus-like sequences in batch 74 of 80
identifying remaining ALUs in batch 76 of 80
identifying remaining ALUs in batch 77 of 80
identifying Simple Repeats in batch 73 of 80
identifying ancient repeats in batch 75 of 80
identifying Simple Repeats in batch 74 of 80
identifying retrovirus-like sequences in batch 75 of 80
identifying most interspersed repeats in batch 76 of 80

Checking for E. coli insertion elements
identifying most interspersed repeats in batch 77 of 80
identifying Simple Repeats in batch 75 of 80
The following E coli IS elements could not be confidently clipped out:
  IS2#ARTEFACT in NC_000913.3frag-78: 33205 - 33848
  IS30#ARTEFACT in NC_000913.3frag-78: 41855 - 41934
  IS30#ARTEFACT in NC_000913.3frag-78: 42637 - 42960
identifying Simple Repeats in batch 78 of 80

Checking for E. coli insertion elements
identifying full-length ALUs in batch 78 of 80
identifying long interspersed repeats in batch 76 of 80
identifying long interspersed repeats in batch 77 of 80
identifying Simple Repeats in batch 79 of 80
identifying full-length interspersed repeats in batch 78 of 80

Checking for E. coli insertion elements
identifying full-length ALUs in batch 79 of 80
identifying ancient repeats in batch 76 of 80
identifying ancient repeats in batch 77 of 80
identifying Simple Repeats in batch 80 of 80
identifying full-length interspersed repeats in batch 79 of 80
identifying full-length ALUs in batch 80 of 80
identifying retrovirus-like sequences in batch 76 of 80
identifying full-length interspersed repeats in batch 80 of 80
identifying remaining ALUs in batch 78 of 80
identifying retrovirus-like sequences in batch 77 of 80
identifying remaining ALUs in batch 79 of 80
identifying Simple Repeats in batch 76 of 80
identifying Simple Repeats in batch 77 of 80
identifying remaining ALUs in batch 80 of 80
identifying most interspersed repeats in batch 78 of 80
identifying most interspersed repeats in batch 79 of 80
identifying long interspersed repeats in batch 78 of 80
identifying most interspersed repeats in batch 80 of 80
identifying ancient repeats in batch 78 of 80
identifying long interspersed repeats in batch 79 of 80
identifying retrovirus-like sequences in batch 78 of 80
identifying long interspersed repeats in batch 80 of 80
identifying ancient repeats in batch 79 of 80
identifying Simple Repeats in batch 78 of 80
identifying retrovirus-like sequences in batch 79 of 80
identifying ancient repeats in batch 80 of 80
identifying Simple Repeats in batch 79 of 80
identifying retrovirus-like sequences in batch 80 of 80
identifying Simple Repeats in batch 80 of 80
processing output: 
cycle 1 
cycle 2 
cycle 3 
cycle 4 
cycle 5 
cycle 6 
cycle 7 
cycle 8 
cycle 9 
cycle 10 
Generating output... 
masking
done
COMMAND="$(echo RepeatMasker -s -a -html -gff -dir RepeatMasker_Output  -pa 8 GCF_000005845.2_ASM584v2_genomic.fna)"
COMMAND="$(echo RepeatMasker -s -a -html -gff -dir RepeatMasker_Output  -pa 8 GCF_000005845.2_ASM584v2_genomic.fna)"
set +v +H +o history
‘RepeatMasker_Output/GCF_000005845.2_ASM584v2_genomic.fna.masked’ -> ‘GCF_000005845.2_ASM584v2_genomic_masked.fasta’
cp: cannot stat ‘.command.log’: No such file or directory
