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FRED-2 / OptiType

Precision HLA typing from next-generation sequencing data
BSD 3-Clause "New" or "Revised" License
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AttributeError: 'IndexedVarWithDomain' object has no attribute 'reset' #13

Closed andrewrech closed 9 years ago

andrewrech commented 9 years ago

Hello,

I received the above error running on example data. Do you have any advice about how I can proceed? Thanks!

Command: python OptiTypePipeline.py -i test/exome/NA11995_SRR766010_1_fished.fastq --verbose --dna --outdir /home/ubuntu/OptiType-master

Config: [MAPPING]

please specify the razerS3 binary path

RAZERS3=/usr/bin/razers3 THREADS=4

[LIBRARIES] RNA_REF=/home/ubuntu/OptiType-master/data/hla_reference_rna.fasta DNA_REF=/home/ubuntu/OptiType-master/data/hla_reference_dna.fasta ALLELES=/home/ubuntu/OptiType-master/data/alleles.h5

[OPTIMIZATION]

the solver has to be supported by Coopr

SOLVER=cbc THREADS=1

Log: 0:00:00.33 Mapping NA11995_SRR766010_1_fished.fastq to GEN reference... 0:00:15.47 Generating binary hit matrix. 0:00:15.47 Loading alleles and read IDs from /home/ubuntu/OptiType-master/2015_09_27_22_16_19/2015_09_27_22_16_19_0.sam... 0:00:16.37 11179 alleles and 1909 reads found. 0:00:16.37 Initializing mapping matrix... 0:00:16.38 1909x11179 mapping matrix initialized. Populating 1344422 hits from SAM file... 10% completed 20% completed 30% completed 40% completed 50% completed 60% completed 70% completed 80% completed 90% completed 100% completed 0:03:20.32 1344422 elements filled. Matrix sparsity: 1 in 15.87

0:03:22.42 temporary pruning of identical rows and columns

0:03:22.51 Size of mtx with unique rows and columns: (434, 1021) 0:03:22.51 determining minimal set of non-overshadowed alleles /home/ubuntu/.local/lib/python2.7/site-packages/pandas/util/decorators.py:13: FutureWarning: diff is deprecated. Use difference instead FutureWarning)

0:03:23.70 Keeping only the minimal number of required alleles (125,)

0:03:23.70 Creating compact model...

0:03:23.83 Initializing OptiType model... Traceback (most recent call last): File "OptiTypePipeline.py", line 322, in result = op.solve(args.enumerate) File "/home/ubuntu/OptiType-master/model.py", line 142, in solve self.__instance.x.reset() AttributeError: 'IndexedVarWithDomain' object has no attribute 'reset'`

andras86 commented 9 years ago

Hi! This is due to Pyomo breaking compatibility in its most recent version. I suggest you downgrade to Pyomo 4.1.10527 for an immediate fix.

andrewrech commented 9 years ago

Thank you, this solved the issue.