[mira_talk] mira 3.0.1 crashes in mapping mode
- From: Jan Paces <hpaces@xxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 11 Mar 2010 16:55:42 +0100
Hi Bastien and all
I found very weird behaviour of mira today, mabe bug? I have 7M
bacterium, 90x coverage on 454, shotgun, 3k library and 8k library. When
I run assembly, everything works well, but when I tried mapping to
cleaned sequence based on newbler assembly, mira crashes with message:
Adding rails to 3 contigs (this may take a while).
Loading data (454) from FASTA files,
Counting sequences in FASTA file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%]
....|.... [90%] ....|.... [100%]
Found 3165081 sequences.
Loading data from FASTA file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%]
....|.... [90%] ....|.... [100%]
Error: read name F49SJEE01CWXC7 present multiple times in readpool!
Error: read name F49SJEE01AKURJ present multiple times in readpool!
Error: read name F49SJEE01DVX43 present multiple times in readpool!
...
Input data are the same (started from the same directory), mira command
lines too except --job mapping versus denovo.
mira --projectin=achromo --projectout=achromo_mira_map_v9a
--job=mapping,accurate,454 -GE:not=6,kcim=yes -CO:np=m9
-OUT:ora=yes,tcpl=100 -AS:urd=on 454_SETTINGS -DP:ure=yes -ED:ace=on
>mira_map_v9.log
mira --projectin=achromo --projectout=achromo_mira_as_v9
--job=denovo,genome,accurate,454 -GE:not=6,kcim=yes -CO:np=a9
-OUT:ora=yes,tcpl=100 -AS:urd=on 454_SETTINGS -DP:ure=yes -ED:ace=on
>mira_as_v9.log
There are no duplicates in input files and assembly runs ok.
Thanks for any help,
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:
