Giter Club home page Giter Club logo

Comments (7)

andras86 avatar andras86 commented on September 28, 2024

I haven't encountered this one before, I'd have to take a look at the intermediate bam file to see what causes it.

from optitype.

alexanderwhatley avatar alexanderwhatley commented on September 28, 2024

I emailed the files to you.

from optitype.

lnovara avatar lnovara commented on September 28, 2024

I am trying to run OptiType from git but I came across the same error originally reported by @alexanderwhatley. Can you help me?

from optitype.

djomlaart avatar djomlaart commented on September 28, 2024

same here. do you know what causes it?

from optitype.

d-henness avatar d-henness commented on September 28, 2024

I am having the same error

from optitype.

yujijun avatar yujijun commented on September 28, 2024

I included optitype into snakemake pipleline, And also got the same error(Invalid constraint expression), Any solution for this problem? @andras86 , thank you!
R2-2-N Error:
Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 64
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 optitype_all
1 optitype_hlatyping
2

[Wed Sep 11 21:54:59 2019]
rule optitype_hlatyping:
    input: analysis/optitype/R2-2-N/R2-2-N.sorted.chr6.end1.fastq, analysis/optitype/R2-2-N/R2-2-N.sorted.chr6.end2.fastq
    output: analysis/optitype/R2-2-N/R2-2-N_result.tsv, analysis/optitype/R2-2-N/R2-2-N_coverage_plot.pdf
    jobid: 4
    benchmark: benchmarks/optitype/R2-2-N/R2-2-N.optitype_hlatyping.txt
    wildcards: sample=R2-2-N

/home/taing/miniconda3/envs/optitype/share/optitype-1.3.2-3/hlatyper.py:239: FutureWarning: from_items is deprecated. Please use DataFrame.from_dict(dict(items), ...) instead. DataFrame.from_dict(OrderedDict(items)) may be used to preserve the key order.
  pos_df = pd.DataFrame.from_items(iter(hits.items())).T
Traceback (most recent call last):
  File "/home/taing/miniconda3/envs/optitype/bin/OptiTypePipeline.py", line 421, in <module>
    result = op.solve(args.enumerate)
  File "/home/taing/miniconda3/envs/optitype/share/optitype-1.3.2-3/model.py", line 188, in solve
    self.__instance.c.add(expr >= 1)
  File "/home/taing/miniconda3/envs/optitype/lib/python2.7/site-packages/pyomo/core/base/constraint.py", line 800, in add
    return Constraint.add(self, self._nconstraints, expr)
  File "/home/taing/miniconda3/envs/optitype/lib/python2.7/site-packages/pyomo/core/base/constraint.py", line 413, in add
    """ % ( expr, expr and "Feasible" or "Infeasible", expr, self.cname(True) ) )
ValueError: 
Invalid constraint expression.  The constraint expression resolved to a
trivial Boolean (False) instead of a Pyomo object.  Please modify your rule
to return Constraint.Infeasible instead of False.

Error thrown for Constraint "c"

[Wed Sep 11 21:55:11 2019]
Error in rule optitype_hlatyping:
    jobid: 4
    output: analysis/optitype/R2-2-N/R2-2-N_result.tsv, analysis/optitype/R2-2-N/R2-2-N_coverage_plot.pdf
    shell:
        source activate /home/taing/miniconda3/envs/optitype/; OptiTypePipeline.py -i analysis/optitype/R2-2-N/R2-2-N.sorted.chr6.end1.fastq analysis/optitype/R2-2-N/R2-2-N.sorted.chr6.end2.fastq --dna -v -o analysis/optitype/R2-2-N/ -p R2-2-N --config cidc_wes/static/optitype/config.ini

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /mnt/ssd/wes/.snakemake/log/2019-09-11T215459.181918.snakemake.log

from optitype.

andras86 avatar andras86 commented on September 28, 2024

I'm afraid this kind of error can only occur if there are no HLA-A, B, or C reads in the sample whatsoever, and hence nothing to type either. Is this from a batch of samples that ran through successfully otherwise?

from optitype.

Related Issues (20)

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.