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tseemann / berokka

🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
GNU General Public License v3.0
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MSG: trunc start,end -- there was no end for 1 #12

Closed tseemann closed 6 years ago

tseemann commented 6 years ago 
*** [5] tig00003742 ***
Using first 3959 bp to BLAST
Writing tig00003742 ( 3959 bp ) to 5.fa
Writing tig00003742 ( 3959 bp ) to 5.head.fa
Running: blastn -query 5.head.fa -subject 5.fa -out 5.bls -evalue 1E-6 -dust no
blastn: 2..3959/3959 aligns to 2..3959/3959 at 98.5 %id
tig00003742 keep 1..0/3959 (remove 3960 bp)

------------- EXCEPTION -------------
MSG: trunc start,end -- there was no end for 1
STACK Bio::PrimarySeqI::trunc /home/linuxbrew/.linuxbrew/Cellar/perl/5.26.1_1/lib/perl5/site_perl/5.26.1/Bio/PrimarySeqI.pm:447
STACK main::check_overhang /home/tseemann/git/berokka/bin/berokka:149
STACK toplevel /home/tseemann/git/berokka/bin/berokka:74
-------------------------------------
tseemann commented 6 years ago

Turns out this is a pacbio control sequence ~ 4000 bp! And it is a palindrome.

I now realise that to circularise the hit must be on strand + / +