Hi all,
I tried running this command again not using our server's queuing system
and got a slightly more informative error. Any ideas?
uqkkocot@barrine3:~> progressiveMauve --seed-family --seed-weight=11
--backbone-output=backbone_output --output=output.mauve seq1
Amphimedon_queenslandica_genomic_scaffolds.fa seq2
Mnemiopsis_leidyi_genomic_scaffolds.fa seq3
Monosiga_brevicollis_genomic_scaffolds.fa seq4
Nematostella_vectensis_genomic_scaffolds.fa seq5
Pleurobrachia_bachei_genomic_scaffolds.fa seq6
Trichoplax_adhaerens_genomic_scaffolds.fa
Exception FileNotOpened thrown from
Unknown() in gnFileSource.cpp 67
Called by Unknown()
Searching with seed pattern 111001001010100100111
Searching with seed pattern 1110101001001010111
Searching with seed pattern 1111001010101001111
done
Floating point exception
Thanks!
Kevin
On 07/06/14 15:34, Kevin Kocot wrote:
Hi all,
I'm interested in examining genomic synteny among several different
animal phyla but I'm getting an error I don't understand. I'm not sure
if this is an issue with progressiveMauve itself or my cluster (The
University of Queensland's Barrine server). Also, I was wondering if
anyone has any thougths on the initial settings I'm trying and if you
think these would be appropriate for this case. I expect a high degree
of genomic re-arrangement among these taxa and, in some cases, a lot
of variation in sequence.
_The script I'm running:_
#!/bin/bash
#PBS -N Mauve -A uq-Biology -m ea -M k.ko...@uq.edu.au
#PBS -l walltime=300:00:00
#PBS -l select=1:ncpus=8:NodeType=large:mem=72g
module load mauve/2.3.1
cd $PBS_O_WORKDIR
progressiveMauve --seed-family --seed-weight=11
--backbone-output=backbone_output --output=output.mauve seq1
Amphimedon_queenslandica_genomic_scaffolds.fa seq2
Mnemiopsis_leidyi_genomic_scaffolds.fa seq3
Monosiga_brevicollis_genomic_scaffolds.fa seq4
Nematostella_vectensis_genomic_scaffolds.fa seq5
Pleurobrachia_bachei_genomic_scaffolds.fa seq6
Trichoplax_adhaerens_genomic_scaffolds.fa
_The error I'm getting:_
########################### Execution Started
#############################
JobId:1134043.paroo3
UserName:uqkkocot
GroupName:uq
ExecutionHost:b10a09
WorkingDir:/var/spool/PBS/mom_priv
###############################################################################
Exception FileNotOpened thrown from
Unknown() in gnFileSource.cpp 67
Called by Unknown()
/var/spool/PBS/mom_priv/jobs/1134043.paroo3.SC: line 7: 15522 Floating
point exceptionprogressiveMauve --seed-family
--backbone-output=backbone_output --output=output.mauve seq1
Amphimedon_queenslandica_genomic_scaffolds.fa seq2
Mnemiopsis_leidyi_genomic_scaffolds.fa seq3
Monosiga_brevicollis_genomic_scaffolds.fa seq4
Nematostella_vectensis_genomic_scaffolds.fa seq5
Pleurobrachia_bachei_genomic_scaffolds.fa seq6
Trichoplax_adhaerens_genomic_scaffolds.fa
########################### Job Execution History
#############################
JobId:1134043.paroo3
UserName:uqkkocot
GroupName:uq
JobName:Mauve
SessionId:15423
ResourcesRequested:mem=64gb,ncpus=1,place=free,walltime=300:00:00
ResourcesUsed:cpupercent=0,cput=00:00:00,mem=1472kb,ncpus=1,vmem=11508kb,walltime=00:00:03
QueueUsed:workq
AccountString:uq-Biology
ExitStatus:136
###############################################################################
Thank you very much!
Kevin Kocot
--
Kevin Kocot, Ph.D.
Postdoctoral Researcher
The University of Queensland
School of Biological Sciences
325 Goddard Building 8
St. Lucia, QLD 4072
Australia
Ph: +61 0402 488 430
--
Kevin Kocot, Ph.D.
Postdoctoral Researcher
The University of Queensland
School of Biological Sciences
325 Goddard Building 8
St. Lucia, QLD 4072
Australia
Ph: +61 0402 488 430
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