Minimus2 - dumpreads

[RLB_84]

Hi everybody here!

I'm trying to merge two de-novo assemblies of the same dataset, obtained with Newbler and Abyss. I'm using Minimus2. Either on my own dataset and on the influenza-A test dataset I get a message like this:

amos/bin/dumpreads influenza-A.bnk -M 0 > influenza-A.ref.seq exited with status: 1

I'm aware that this is a kinda generic error, but can anyone help out with this?

Thanks to all,
Domenico

[ians]

I know this is kind of old, but this seems to be a fix:

http://sourceforge.net/tracker/?func=detail&aid=3204724&group_id=134326&atid=729719

[sagarutturkar]

Minimus 2 issues

I was getting errors at various steps and I am explaining how i resolved them. This might be useful for someone trying to run minimus for first time.

1. I got error at step 12. cannot write/find bnk file
here you need to make sure that your fasta files does not have any special characters and fasta headers are not longer than 1024 bytes (note bytes not characters). Fasta header such as >contig1 should be kept and everything else should be discarded. Special character _ and > is allowed but not any others such as = or .(dot). Also make sure any of the folder names do not have special characters.

2. Got error at step 21: unable to run show-coordinates
I found this was mainly because of file path. The default minimus2 has file path:

DELTAFILTER = /usr/local/bin/delta-filter
SHOWCOORDS = /usr/local/bin/show-coords

While

my installed directory contains these commands at
DELTAFILTER = /usr/local/MUMmer3.22/delta-filter
SHOWCOORDS = /usr/local/MUMmer3.22/show-coords

You need to update path in minimus2 file.

Also its helpful to check post

http://seqanswers.com/forums/showthread.php?t=6367

if you are using contigs containing lot of N's

Hope this helps.