genpipes/4.1.2 Error

[Marco]

Hello ...

I am trying to figure out what I am doing wrong here ...

umask 0002

module load mugqic/python/3.9.1
module load mugqic/genpipes/4.1.2

HOST="cedar";
DNSDOMAIN="cedar.computecanada.ca";
export MUGQIC_INSTALL_HOME=/cvmfs/soft.mugqic/CentOS6
export MUGQIC_INSTALL_HOME_DEV=/project/6007512/C3G/analyste_dev
module use $MUGQIC_INSTALL_HOME/modulefiles $MUGQIC_INSTALL_HOME_DEV/modulefiles
export JOB_MAIL=[deleted]
export RAP_ID=[deleted]

cat << EOF > readset.dnaseq.txt
Sample        Readset        Library        RunType        Run        Lane        Adapter1        Adapter2        QualityOffset        BED        FASTQ1        FASTQ2        BAM
HEK-MCB1        HEK-MCB1        1        PAIRED_END        1        1        AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC        AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT        33                ./HEK-MCB1_1.fq         ./HEK-MCB1_2.fq        
HEK-MCB2        HEK-MCB2        1        PAIRED_END        1        1        AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC        AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT        33                ./HEK-MCB2b_1.fq         ./HEK-MCB2b_2.fq        
EOF

#!bash
$MUGQIC_PIPELINES_HOME/pipelines/dnaseq/dnaseq.py -t sv -j slurm --config $MUGQIC_PIPELINES_HOME/pipelines/dnaseq/dnaseq.cedar.ini $MUGQIC_PIPELINES_HOME/resources/genomes/config/Homo_sapiens.GRCh38.ini -r readset.dnaseq.txt -s 2-24 > ./dnaseqCommands_mugqic.sh

Traceback (most recent call last):
  File "/cvmfs/soft.mugqic/CentOS6/software/genpipes/genpipes-4.1.2/pipelines/dnaseq/dnaseq.py", line 3873, in <module>
    DnaSeq(protocol=['mugqic', 'mpileup', "light", "sv"])
  File "/cvmfs/soft.mugqic/CentOS6/software/genpipes/genpipes-4.1.2/pipelines/dnaseq/dnaseq.py", line 3866, in __init__
    super(DnaSeq, self).__init__(protocol)
  File "/cvmfs/soft.mugqic/CentOS6/software/genpipes/genpipes-4.1.2/pipelines/dnaseq/dnaseq.py", line 116, in __init__
    super(DnaSeqRaw, self).__init__(protocol)
  File "/cvmfs/soft.mugqic/CentOS6/software/genpipes/genpipes-4.1.2/pipelines/common.py", line 131, in __init__
    super(Illumina, self).__init__(protocol)
  File "/cvmfs/soft.mugqic/CentOS6/software/genpipes/genpipes-4.1.2/pipelines/common.py", line 66, in __init__
    super(MUGQICPipeline, self).__init__()
  File "/cvmfs/soft.mugqic/CentOS6/software/genpipes/genpipes-4.1.2/core/pipeline.py", line 101, in __init__
    config.parse_files(self.args.config)
  File "/cvmfs/soft.mugqic/CentOS6/software/genpipes/genpipes-4.1.2/core/config.py", line 62, in parse_files
    self.check_modules()
  File "/cvmfs/soft.mugqic/CentOS6/software/genpipes/genpipes-4.1.2/core/config.py", line 71, in check_modules
    for name, value in self.items(section):
  File "/cvmfs/soft.mugqic/CentOS6/software/python/Python-3.9.1/lib/python3.9/configparser.py", line 859, in items
    return [(option, value_getter(option)) for option in orig_keys]
  File "/cvmfs/soft.mugqic/CentOS6/software/python/Python-3.9.1/lib/python3.9/configparser.py", line 859, in <listcomp>
    return [(option, value_getter(option)) for option in orig_keys]
  File "/cvmfs/soft.mugqic/CentOS6/software/python/Python-3.9.1/lib/python3.9/configparser.py", line 855, in <lambda>
    value_getter = lambda option: self._interpolation.before_get(self,
  File "/cvmfs/soft.mugqic/CentOS6/software/python/Python-3.9.1/lib/python3.9/configparser.py", line 395, in before_get
    self._interpolate_some(parser, option, L, value, section, defaults, 1)
  File "/cvmfs/soft.mugqic/CentOS6/software/python/Python-3.9.1/lib/python3.9/configparser.py", line 434, in _interpolate_some
    raise InterpolationMissingOptionError(
configparser.InterpolationMissingOptionError: Bad value substitution: option 'gnomad_exome' in section 'picard_sam_to_fastq' contains an interpolation key 'assembly_dir' which is not a valid option name. Raw value: '%(assembly_dir)s/annotations/%(scientific_name)s.%(assembly)s.gnomad.exomes.r2.0.2.sites.no-VEP.nohist.tidy.vcf.gz'

It seems to me this error refers to Step 1 (picard_sam_to_fastq), but I am skipping step 1.

Thanks for suggestions.

- Marco.

[GenPipes]

Hi Marco,

You also need the .base.ini in your command line.

Please try the following : 

$MUGQIC_PIPELINES_HOME/pipelines/dnaseq/dnaseq.py -t sv -j slurm --config $MUGQIC_PIPELINES_HOME/pipelines/dnaseq/dnaseq.base.ini $MUGQIC_PIPELINES_HOME/pipelines/dnaseq/dnaseq.cedar.ini $MUGQIC_PIPELINES_HOME/resources/genomes/config/Homo_sapiens.GRCh38.ini -r readset.dnaseq.txt -s 2-24 > ./dnaseqCommands_mugqic.sh

Regards,

Edouard

[Marco]

Hello ...

Thanks for that suggestion. It worked, one step further. But now I am getting this error ...

Sample        Readset        Library        RunType        Run        Lane        Adapter1        Adapter2        QualityOffset        BED        FASTQ1        FASTQ2        BAM

HEK-MCB1        Readset1        1        PAIRED_END        1        1        AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC        AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT        33                ./HEK-MCB1_1.fq.gz        ./HEK-MCB1_2.fq.gz        
HEK-MCB2        Readset1        1        PAIRED_END        1        1        AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC        AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT        33                ./HEK-MCB2_1.fq.gz        ./HEK-MCB2_2.fq.gz        

INFO:core.config:Check modules...
INFO:core.config:module check finished

INFO:core.pipeline:Create jobs for step skewer_trimming...
INFO:bfx.readset:Parse Illumina readset file readset.dnaseq.txt ...

Traceback (most recent call last):
  File "/cvmfs/soft.mugqic/CentOS6/software/genpipes/genpipes-4.1.2/pipelines/dnaseq/dnaseq.py", line 3873, in <module>
    DnaSeq(protocol=['mugqic', 'mpileup', "light", "sv"])
  File "/cvmfs/soft.mugqic/CentOS6/software/genpipes/genpipes-4.1.2/pipelines/dnaseq/dnaseq.py", line 3866, in __init__
    super(DnaSeq, self).__init__(protocol)
  File "/cvmfs/soft.mugqic/CentOS6/software/genpipes/genpipes-4.1.2/pipelines/dnaseq/dnaseq.py", line 116, in __init__
    super(DnaSeqRaw, self).__init__(protocol)
  File "/cvmfs/soft.mugqic/CentOS6/software/genpipes/genpipes-4.1.2/pipelines/common.py", line 131, in __init__
    super(Illumina, self).__init__(protocol)
  File "/cvmfs/soft.mugqic/CentOS6/software/genpipes/genpipes-4.1.2/pipelines/common.py", line 66, in __init__
    super(MUGQICPipeline, self).__init__()

  File "/cvmfs/soft.mugqic/CentOS6/software/genpipes/genpipes-4.1.2/core/pipeline.py", line 165, in __init__
    self.create_jobs()
  File "/cvmfs/soft.mugqic/CentOS6/software/genpipes/genpipes-4.1.2/core/pipeline.py", line 372, in create_jobs
    jobs = step.create_jobs()
  File "/cvmfs/soft.mugqic/CentOS6/software/genpipes/genpipes-4.1.2/pipelines/dnaseq/dnaseq.py", line 247, in skewer_trimming
    for readset in self.readsets:
  File "/cvmfs/soft.mugqic/CentOS6/software/genpipes/genpipes-4.1.2/pipelines/common.py", line 137, in readsets
    self._readsets = parse_illumina_readset_file(self.args.readsets.name)
  File "/cvmfs/soft.mugqic/CentOS6/software/genpipes/genpipes-4.1.2/bfx/readset.py", line 162, in parse_illumina_readset_file
    dup_found_message = checkDuplicateReadsets(illumina_readset_file)
  File "/cvmfs/soft.mugqic/CentOS6/software/genpipes/genpipes-4.1.2/bfx/readset.py", line 612, in checkDuplicateReadsets
    writer.writeheader()
  File "/cvmfs/soft.mugqic/CentOS6/software/python/Python-3.9.1/lib/python3.9/csv.py", line 143, in writeheader
    return self.writerow(header)
  File "/cvmfs/soft.mugqic/CentOS6/software/python/Python-3.9.1/lib/python3.9/csv.py", line 154, in writerow
    return self.writer.writerow(self._dict_to_list(rowdict))
TypeError: a bytes-like object is required, not 'str'