AttributeError: 'Index' object has no attribute 'difference'
renyuan01 opened this issue · comments
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'
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
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