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hoelzer-lab / ribap

A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
GNU General Public License v3.0
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GLPSOL: Multiple use of variable 'x_A1h_A1t' not allowed #11

Closed hoelzer closed 1 year ago

hoelzer commented 4 years ago

Test data: 36 Mycoplasma bovis assemblies

Run on a HPC w/ LSF (using dockers)

Command:

glpsol --lp ilp/DHBIBIFB-vs-FNBNKPCI_0.ilp --mipgap 0.01 --pcost --cuts --memlim 16834 --tmlim 240 -o solved/DHBIBIFB-vs-FNBNKPCI_0.sol

Error:

Command output:
  GLPSOL: GLPK LP/MIP Solver, v4.65
  Parameter(s) specified in the command line:
   --lp ilp/DHBIBIFB-vs-FNBNKPCI_0.ilp --mipgap 0.01 --pcost --cuts --memlim
   16834 --tmlim 240 -o solved/DHBIBIFB-vs-FNBNKPCI_0.sol
  Reading problem data from 'ilp/DHBIBIFB-vs-FNBNKPCI_0.ilp'...
  ilp/DHBIBIFB-vs-FNBNKPCI_0.ilp:911: multiple use of variable 'x_A1h_A1t' not allowed
  CPLEX LP file processing error

Looking for x_A1h_A1t in the .ilp file:

grep x_A1h_A1t /hps/nobackup2/metagenomics/mhoelzer/nextflow-work-mhoelzer/ribap/8b/9dcf15beab58ae5c3644c9fb48c93c/ilp/DHBIBIFB-vs-FNBNKPCI_0.ilp 
c2849: x_A1t_B849t + x_A1h_A1t = 1
c2850: x_A1h_B849h + x_A1h_A1t = 1
c3719: x_A1h_A1t + x_B849h_B849t <= 1
c14378: y_A1h - y_A1t  + 1764 x_A1h_A1t <= 1764
c14379: y_A1t - y_A1h  + 1764 x_A1h_A1t <= 1764
c16131: x_A1h_A1t - x_A1h_A1t - b_A1 <= 0
x_A1h_A1t

I can't tell if this is fine or not.

hoelzer commented 4 years ago

For later reference: I can reproduce this error on the EBI cluster:

cd /hps/research/finn/mhoelzer/ribap/mbovis
nextflow run hoelzer-lab/ribap -r v0.3 --fasta 'genomes/*.fasta' -profile lsf --cachedir /hps/nobackup2/singularity/mhoelzer/ --workdir work --output tmlim240 --tmlim 240 --tree --gcode 4 -resume

Currently, the error is ignored but we can change this code snippet and -resume the run to reproduce the error using the above command.

klamkiew commented 1 year ago

I remember looking into this back then, but I have no idea what the conclusion was. Past-Me labeled this as invalid!? I've seen many commits on 31.05.2020 from both of us. Maybe we fixed it back then?

hoelzer commented 1 year ago

Uff yeah, might be just solved based on all the recent changes. I would close this - for now.