ConfigParser.NoSectionError: No section: 'LIBRARIES'

[jungminchoilab]

Hello,

I ran the script with the provided exome test files and got these error messages. I would greatly appreciate it if you can have a look and help me troubleshoot the issues.

[jc2545@login-0-1 exome]$ python ~/programs/OptiType-master/OptiTypePipeline.py -i NA11995_SRR766010_1_fished.fastq NA11995_SRR766010_2_fished.fastq -d -v -o .
Traceback (most recent call last):
  File "/home/jc2545/programs/OptiType-master/OptiTypePipeline.py", line 195, in <module>
ALLELE_HDF = config.get("LIBRARIES", "ALLELES")
  File "/home/jc2545/python/lib/python2.7/ConfigParser.py", line 607, in get
raise NoSectionError(section)
ConfigParser.NoSectionError: No section: 'LIBRARIES'

Here is my config.ini file

[jc2545@login-0-0 OptiType-master]$ cat config.ini 
[MAPPING]
#please specify the razerS3 binary path
RAZERS3=/home/jc2545/programs/razers3-3.4.0-Linux-x86_64/bin/razers3
THREADS=8

[LIBRARIES]
RNA_REF=./data/hla_reference_rna.fasta
DNA_REF=./data/hla_reference_dna.fasta
ALLELES=./data/alleles.h5

[OPTIMIZATION]
#the solver has to be supported by Coopr
SOLVER=cbc
THREADS=1

I believe all the required softwares and libraries are installed.

[jc2545@login-0-1 exome]$ python ~/programs/OptiType-master/OptiTypePipeline.py --help
usage: OptiType [-h] --input INPUT [INPUT ...] (--rna | --dna) [--beta BETA]
            [--enumerate ENUMERATE] --outdir OUTDIR [--verbose]

OptiType: 4-digit HLA typer

optional arguments:
  -h, --help            show this help message and exit
  --input INPUT [INPUT ...], -i INPUT [INPUT ...]
                        Fastq files with fished HLA reads. Max two files (for
                        paired-end)
  --rna, -r             Specifiying the mapped data as RNA.
  --dna, -d             Specifiying the mapped data as DNA.
  --beta BETA, -b BETA  The beta value for for homozygosity detection.
  --enumerate ENUMERATE, -e ENUMERATE
                         The number of enumerations.
  --outdir OUTDIR, -o OUTDIR
                        Specifies the out directory to which all files should
                        be written
  --verbose, -v         Set verbose mode on.

[b-schubert]

Hi,

We are using relative paths within OptiType. You either have to call OptiType within ~/programs/OptiType-master/ or you have to change all relative paths to absolute paths within the config.ini and OptiTypePipeline.py.

That should resolve the exception.

Best, Benni

[jungminchoilab]

Hi Benni,

Thank so much for your prompt solution.

Best, Jungmin