Comments (7)
I haven't encountered this one before, I'd have to take a look at the intermediate bam file to see what causes it.
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I emailed the files to you.
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I am trying to run OptiType from git but I came across the same error originally reported by @alexanderwhatley. Can you help me?
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same here. do you know what causes it?
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I am having the same error
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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
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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?
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Related Issues (20)
- OptiType returns ValueError with some samples while running just fine with others
- could not open alignment file HOT 4
- output file column description
- error using docker
- Hi dear @andras86 , What's the meanning for "introns from " as picture beblow? I found it apprearing in https://github.com/FRED-2/OptiType/blob/master/hlatyper.py HOT 1
- Does OptiType only predict alleles in "freq_alleles" HOT 1
- Is it based on hg38 genome? HOT 3
- ValueError: too many values to unpack
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- Want to use Optitype HLA results as input file for pVACseq, if someone could provide suggestion? HOT 2
- Installation problem with pyomo module HOT 1
- this team is no longer maintained HOT 1
- HLA typing 10x scRNA-seq data with Optitype
- unpaired reads, no mismatches, ambiguous HOT 1
- Razers3 being slow HOT 1
- Issue with downloading OptiType docker image HOT 1
- core dumped bad_alloc in seqan HOT 6
- Bam file to prefilter reads HOT 1
- IOError: [Errno 2] could not open alignment file
- OptiType Fails to Open Intermediate BAM File
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