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
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