NoSectionError: No section: 'GENERAL'

[marcovth]

Unfortunately, on two different linux machines, I am getting the same python error with clean installs ... BTW, I am getting the exact same error when I run the docker instance through singularity.

C >> 1

---

    *** In this part you can specify your data-set location ***

If you have data-set in pair-end mode, you have to give the pattern of extension.

ERROR:root:Traceback (most recent call last): File "/project/6029819/marcovth/ecoli/MethylStar/src/py/configuration.py", line 219, in raw_dataset if confirm("GENERAL", "raw_dataset", 3): File "/project/6029819/marcovth/ecoli/MethylStar/src/py/configuration.py", line 191, in confirm str_conf = read_config(config_section, config_value) File "/project/6029819/marcovth/ecoli/MethylStar/src/py/globalParameters.py", line 87, in read_config val_str = config.get(section, get_string) File "/home/marcovth/miniconda3/envs/MethylStar/lib/python2.7/ConfigParser.py", line 607, in get raise NoSectionError(section) NoSectionError: No section: 'GENERAL'

Something is going wrong... please run again.

[marcovth]

Is there a way to start MethylStar through commandline parameters? I can not run it through sbatch as an interactive program.

[shahryary]

Hi @marcovth

Thank you very much for using our pipeline, I updated the Docker image, please download and re-run again. We are still working on scripts that you can submit through the queue-based system.

[marcovth]

Thanks for the service.

I had to make some adjustments but I got my ecoli test-run started with singularity instead of docker ...

... Docker image

// wget http://jlabdata.org/methylstar.tar.gz

Can't run MethylStar with sbatch, therefore Interactive instance is the only option ...

salloc --time=12:0:0 --ntasks=48 --mem-per-cpu=3G -

module load singularity

singularity build methylstar.sif docker-archive://methylstar.tar.gz

export SINGULARITY_BUILD_PROCESSORS=48 singularity run -B /project/6029819/marcovth/ecoli/:/ecoli methylstar.sif

Perl is giving warnings, this should fix that ...

export LANGUAGE=en_US.UTF-8 export LANG=en_US.UTF-8 export LC_ALL=en_US.UTF-8 locale-gen en_US.UTF-8

cd /ecoli/MethylStar ./run.py

Trimommatic, fastqc working well. bismark currently running.

[GENERAL] firstRun=false currversion=1.1.1 raw_dataset=/ecoli/fastq result_pipeline=/ecoli/mstar_results genome_ref=/ecoli/Genome genome_name=Ecoli.fa genome_type=Others docker_mode=false parallel_mode=true npar=0 fastq_path=/home/software/FastQC/fastqc number_of_dataset=2 dataset_size=9.7 pairs_mode=true first_pattern=_1.fastq.gz secnd_pattern=_2.fastq.gz

[Trimmomatic] java_path=/usr/bin/java trim_path=/home/software/Trimmomatic-0.38 trim_jar=/home/software/Trimmomatic-0.38/trimmomatic-0.38.jar dir_adap=$trim_path/adapters name_adap=/home/software/Trimmomatic-0.38/adapters/TruSeq3-SE.fa end_mode=PE ill_clip=1:30:9 LEADING=20 TRAILING=20 SLIDINGWINDOW=4:20 MINLEN=36 n_th=8

[Bismark] bismark_path=/home/software/Bismark-0.20.1 samtools_path=/home/software/samtools-1.9/samtools bedtools_path=/home/marcovth/miniconda3/envs/MethylStar/bin/bedtools modified_time=1539787258 bis_parallel=8 buf_size=40 Nthreads=48 nucleotide=false intermediate_files=false run_pair_bismark=true deduplicate=-p methextractor=-p del_inter_file=true single_cell=false directional=

Warnings ....

perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LANG = "en_CA.UTF-8" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C"). perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LANG = "en_CA.UTF-8" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C"). Academic tradition requires you to cite works you base your article on. When using programs that use GNU Parallel to process data for publication please cite:

O. Tange (2011): GNU Parallel - The Command-Line Power Tool, ;login: The USENIX Magazine, February 2011:42-47.

This helps funding further development; AND IT WON'T COST YOU A CENT. If you pay 10000 EUR you should feel free to use GNU Parallel without citing.

To silence this citation notice: run 'parallel --citation'.

[shahryary]

Ignore the warning output, It's just some output when trying to install GNU-parallel.