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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: 'Index' object has no attribute 'difference' #115

Open renyuan01 opened 4 years ago

renyuan01 commented 4 years ago

conda create -n optitype python=2.7.3 conda install -n optitype -c bioconda optitype conda activate optitype bam=/home/ry/analysis/data/optitype/bam raw=/home/ry/analysis/data/optitype/raw fastq=/home/ry/analysis/data/optitype/fastq hla=/home/ry/analysis/data/optitype/hla dnaref=/home/ry/analysis/data/optitype/hlareference/hla_reference_dna.fasta OptiTypePipeline.py -i $fastq/GYH1.fastq $fastq/GYH2.fastq --dna -v -o $hla -p GYH.optitype.dna

mapping with 11 threads...

0:00:00.36 Mapping GYH1.fastq to GEN reference...

0:00:32.76 Mapping GYH2.fastq to GEN reference...

0:01:06.82 Generating binary hit matrix. 0:01:06.83 Loading /home/ry/analysis/data/optitype/hla/2020_09_03_21_50_24_1.bam started. Number of HLA reads loaded (updated every thousand): 1K...2K...3K...4K...5K...6K...7K...8K...9K...10K...11K... 0:01:09.90 11460 reads loaded. Creating dataframe... 0:01:10.22 Dataframes created. Shape: 11460 x 11179, hits: 2224373 (2224373), sparsity: 1 in 57.59 0:01:11.55 Loading /home/ry/analysis/data/optitype/hla/2020_09_03_21_50_24_2.bam started. Number of HLA reads loaded (updated every thousand): 1K...2K...3K...4K...5K...6K...7K...8K...9K...10K...11K... 0:01:14.45 11318 reads loaded. Creating dataframe... 0:01:14.77 Dataframes created. Shape: 11318 x 11179, hits: 2149552 (2149552), sparsity: 1 in 58.86

Traceback (most recent call last): File "/home/ry/miniconda3/envs/optitype/bin/OptiTypePipeline.py", line 347, in binary_p, binary_mis, binary_un = ht.create_paired_matrix(binary1, binary2) File "/home/ry/miniconda3/envs/optitype/share/optitype-1.3.2-1/hlatyper.py", line 518, in create_paired_matrix only_1 = binary_1.index.difference(binary_2.index) AttributeError: 'Index' object has no attribute 'difference'

renyuan01 commented 4 years ago

conda list

packages in environment at /home/ry/miniconda3/envs/optitype:

#

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_gnu conda-forge bzip2 1.0.8 h516909a_3 conda-forge cairo 1.12.2 0 defaults certifi 2016.9.26 py27_0 conda-forge dateutil 2.4.1 py27_0 defaults freetype 2.4.10 0 defaults future 0.18.2 py27_0 conda-forge glpk 4.57 0 bioconda hdf5 1.8.9 1 defaults libgcc 7.2.0 h69d50b8_2 conda-forge libgcc-ng 9.3.0 h24d8f2e_16 conda-forge libgomp 9.3.0 h24d8f2e_16 conda-forge libstdcxx-ng 9.3.0 hdf63c60_16 conda-forge matplotlib 1.1.1 np17py27_1 defaults ncurses 5.9 10 conda-forge nose 1.3.7 py27_1003 conda-forge numexpr 2.2.2 np17py27_1 defaults numpy 1.7.1 py27_2 defaults openssl 1.0.1k 1 defaults optitype 1.3.2 py27_1 bioconda pandas 0.13.0 np17py27_0 defaults pip 20.0.2 py27_1 conda-forge pixman 0.26.2 0 defaults ply 3.11 py_1 conda-forge py2cairo 1.10.0 py27_1 defaults pyomo 4.1.10527 py27_1 bioconda pysam 0.8.4 py27_0 bioconda pytables 3.0.0 np17py27_1 defaults python 2.7.3 7 defaults pytz 2020.1 pyh9f0ad1d_0 conda-forge pyutilib 5.1.3556 py27_0 bioconda razers3 3.5.8 hb7ba0dd_0 bioconda readline 6.2 0 conda-forge samtools 1.3.1 0 bioconda setuptools 36.4.0 py27_1 defaults six 1.15.0 pyh9f0ad1d_0 conda-forge sqlite 3.13.0 1 conda-forge system 5.8 2 defaults tk 8.5.18 0 defaults wheel 0.35.1 pyh9f0ad1d_0 conda-forge zlib 1.2.11 h516909a_1009 conda-forge

bobojin46 commented 1 year ago

Hi I ran into this erro,too. Did you solve that problem now? Can you tell me the solution if possible? thank u very much