[AMOS-help] Fwd: help in running minimus2

[Domenico S. <dom...@gm...>]

---------- Forwarded message ----------
From: Domenico Simone <dom...@gm...>
Date: 2011/12/8
Subject: help in running minimus2
To: amo...@li...


hi everybody,

I tried to merge two contig datasets obtained with Newbler and Abyss. I
followed the default pipeline involving

cat S1.seq S2.seq > S1-S2.seq
toAmos -s S1-S2.seq -o S1-S2.afg

[this didn't report me any error, just the message: Max ID: 2736]

then run 'minimus2 S1-S2 -D REFCOUNT=261' as the first assembly contains
261 contigs.

the log reports:

START DATE: Thu Dec  8 13:05:17 2011
Bank is: newbler+abyss.bnk
    0%                                            100%
AFG ERROR: Failed to obtain bank IFO file lock, Operation timed out
  could not open 'UNV' bank, all messages ignored
ERROR: Failed to obtain bank IFO file lock, Operation timed out
  could not open 'LIB' bank, all messages ignored
ERROR: Failed to obtain bank IFO file lock, Operation timed out
  could not open 'FRG' bank, all messages ignored
ERROR: Failed to obtain bank IFO file lock, Operation timed out
  could not open 'RED' bank, all messages ignored
..................................................
Messages read: 1824
Objects added: 0
Objects deleted: 0
Objects replaced: 0
END DATE:   Thu Dec  8 13:05:37 2011
!!! 2011-12-08 13:05:37  Command:
/Users/domenico/Library/Tools/amos/bin/bank-transact -c -z -b
newbler+abyss.bnk -m newbler+abyss.afg exited with status: 1
!!! END - Elapsed time: 0d 0h 0m 21s

What am I missing? I re-formatted the fasta files in any way: renamed the
contigs in the S1-S2.fa file in order to have only one numbering (Newbler
contigs were: "contig00001..", Abyss contigs were "0", "1" and so on); for
each contig, I put the sequence on a single line.

Thanks for your kind support

-- 
Domenico Simone, PhD student

Dept. of Biochemistry and Molecular Biology "Ernesto Quagliarello",
University of Bari
via Orabona 4, 70126 - Bari (Italy)
Tel./Fax +390805442399



-- 
Domenico Simone, PhD student

Dept. of Biochemistry and Molecular Biology "Ernesto Quagliarello",
University of Bari
via Orabona 4, 70126 - Bari (Italy)
Tel./Fax +390805442399