It looks like you are overwriting an existing _assembly directory. Try
deleting Sm-Genome-PacBio_assembly, or use a different project name, or
move to a different parent directory before executing mira.
On Thu, Aug 13, 2015 at 7:45 AM, Elton Vasconcelos <eltonjrv@xxxxxxxxx>
wrote:
Hello Mira Folks,
I am getting the following error message:
###########################
A 'standard' exception occured (that's NOT normal):
boost::filesystem::create_symlink: File exists:
"./temp/Sm-Genome-PacBio_d_tmp_9gmBGD_4MS2lw",
"Sm-Genome-PacBio_assembly/Sm-Genome-PacBio_d_tmp"
If the cause is not immediatly obvious, please contact: bach@xxxxxxxxxxxx
For general help, you will probably get a quicker response on the
MIRA talk mailing list
than if you mailed the author directly.
To report bugs or ask for features, please use the SourceForge ticketing
system at:
http://sourceforge.net/p/mira-assembler/tickets/
This ensures that requests do not get lost.
Aborted (core dumped)
Failure, wrapped MIRA process aborted.
############################
And this is my manifest.conf:
#############################
project = Sm-Genome-PacBio
job = genome,denovo,accurate
#job = genome,mapping,accurate #if a hybrid assembly
parameters = -DI:trt=./temp -NW:cmrnl=warn \
PCBIOHQ_SETTINGS -CO:mrpg=10 -CL:lccf=off lccb=off
#parameters = -NW:cnfs=warn
### Illumina paired-end data
#readgroup = DataForShotgunIlluminaPairedLib
#data = ../all_R1-trimmed_paired.fastq ../all_R2-trimmed_paired.fastq
#template_size = 200 500 autorefine #if the user knows about the
insert size
#segment_placement = ---> <--- #if the user knows about reads
orientation
#autopairing
#technology = solexa
### PacBioHQ Data
#parameters = PCBIOHQ_SETTINGS -CO:mrpg=10
readgroup = DataForShotGunPacBioHQ
technology=pcbiohq
data=../pacbio-corrected-hybrid-reads_ready4Mira.fna
default_qual=30
##############################
Any clue to solve that issue?
Thanks,
Elton
--
Elton Vasconcelos, DVM, PhD
Post-doc at Verjovski-Almeida Lab
Department of Biochemistry - Institute of Chemistry
University of Sao Paulo, Brazil
