[mira_talk] reading fasta files

Hi Bastien and all,

I assembled bacterial genome (~7M, 30 coverage on 454 not paired). Today
I just for curiosity added fasta files from that particular bug which
are already known from genbank (~200 short records, marginal part of the
genome, not suitable for mapping), but without success. It looks I have
problem with reading sanger fasta files, but I can't figure out, how to
overcome it.

Details follows:

Shortly after starting mira:

mira -project=mira_v3 -job=denovo,genome,sanger,454,accurate
COMMON_SETTINGS -GE:not=8

i got:

<code>
Short length: FS4OOG301DEWUX (454): only 39 good bases, need: 40. No
paired end partner, rejected.
Short length: FS4OOG301BF1EN (454): only 38 good bases, need: 40. No
paired end partner, rejected.
Short length: FS4OOG301C692T (454): only 38 good bases, need: 40. No
paired end partner, rejected.
Short length: FS4OOG301CAS2J (454): only 38 good bases, need: 40. No
paired end partner, rejected.
Short length: ^C
[1]+  Floating point exception
</code>

however, reading fasta files seems to work fine:

<code>
Loading data normal (probably Sanger type) from FASTA files,
Counting sequences in FASTA file:
Loading sequence data from FASTA file mira_v3_in.sanger.fasta:
Could not find FASTA quality file mira_v3_in.sanger.fasta.qual, using
default qualities for all reads.
Done.
Loaded 207 reads, 0 of which have quality accounted for.
</code>

but clipping went wrong for all sanger reads:

<code>
Short length: a001 (san): only 0 good bases, need: 80. No paired end
partner, rejected.
</code>

Thanks for any suggestions,

Jan

-- 
You have received this mail because you are subscribed to the mira_talk mailing 
list. For information on how to subscribe or unsubscribe, please visit 
http://www.chevreux.org/mira_mailinglists.html

Other related posts: