Pyomo-supported ILP solver

Hello,

OptiType returned the following message while calling the module model.py:

Invalid option '-s'; try /group/bioinformatics/software/GLPK/4.61/bin/glpsol --help
ERROR: "[base]/site-packages/pyomo/opt/base/solvers.py", 599, solve
	Solver (asl) returned non-zero return code (1)
ERROR: "[base]/site-packages/pyomo/opt/base/solvers.py", 602, solve
	See the solver log above for diagnostic information.

This is my command:

module load anaconda3
source activate python2.7

module load GLPK/4.61 HDF5/1.10.0-patch1 samtools/1.2 bwa/0.7.15 sambamba/0.5.6

python ./OptiTypePipeline.py -i ./test/exome/NA11995_SRR766010_1_fished.fastq ./test/exome/NA11995_SRR766010_2_fished.fastq -o test -d -v

source deactivate

I was not able to install RazerS and CPLEX on our server, hence went for bwa and GLPK instead. I modified OptiTypePipeline.py a little bit to take in bwa alignment commands instead of the default RazerS .

The command-line solver for GLPK is glpsol, which I also changed in config.ini. Could that be the reason why the error was reported? The modified OptiTypePipeline.py, config, commands and log files are attached here if helpful myfiles.zip

Any help would be highly appreciated. Thanks much in advance 😃

Best, Riyue (Sunny) The University of Chicago

[riyuebao]

Hi just want to follow up that I have run all my samples by OptiType and the results look great. For each exome it took 5 to 15 mins to run with 8 threads from raw fastq to final output - super fast!

[riyuebao]

Thanks Benjamin. Yup that was due to the default alignment settings of bwa, which does not report all best alignments and filter out multitargets, and is not suitable for mapping to HLA loci.

The issue with RazerS3’s installation was the gcc version - but our system adm helped fix it yesterday!! 😃 I compiled yara and razers3 and they both worked (BTW if anyone is interested in compiling individual tools from seqan, the installation instructions on yara github is super helpful).

This is the new result generated with aligner razers3: dna fastq files & -d: 2017_04_19_12_50_43_coverage_plot.pdf

	A1	A2	B1	B2	C1	C2	Reads	Objective
0	A*01:01	A*01:01	B*08:01	B*57:01	C*07:01	C*06:02	1156.0	1135.192

rna fastq files & -r: 2017_04_19_12_53_22_coverage_plot.pdf

	A1	A2	B1	B2	C1	C2	Reads	Objective
0	A*31:01	A*68:01	B*40:01	B*51:01	C*15:02	C*03:04	132.0	128.436

The results make a lot more sense now … 😃