Can't concatenate dataframes during edge_flagging
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I've been trying to run the tool on some mouse data and have been met with the following error once I reach the --HITindex step
Traceback (most recent call last):
File "HITindex_classify.py", line 589, in <module>
HITdict, param = edge_flagging(HITdict)
File "HITindex_classify.py", line 345, in edge_flagging
flaggingdata = pd.concat(flaggingdata, ignore_index=True)
File "/home/kskrick/miniconda2/envs/hits/lib/python3.6/site-packages/pandas/core/reshape/concat.py", line 284, in concat
sort=sort,
File "/home/kskrick/miniconda2/envs/hits/lib/python3.6/site-packages/pandas/core/reshape/concat.py", line 331, in __init__
raise ValueError("No objects to concatenate")
ValueError: No objects to concatenate
I get this running
HITindex_classify.py --HITindex --juncbam junction.bam --readtype paired --readstrand fr-unstrand --bed gencode_vM31.hits_ss3-50ss5-20.buffer --overlap 10 --readnum 5 --outname testHIT
after I've extracted junction reads using HITindex_classify.py --junctionReads.
I've checked the HITdict object and it contains the gene ids from the gtf file. The junction read files contain reads and the annotation step was completed without any problems.
The line where it breaks seems to only have one dataframe it's trying to concatenate.
# concatenate dataframes
flaggingdata = pd.concat(flaggingdata, ignore_index=True)
Am I missing something? I've tried to comment out the line and add HITdict to the function to no avail. Appreciate any help!
Conda environment info below - I tried to match the development versions for each package but for some I could only find later versions with stable conda packages (pymc3 is a big problem in this regard).
# packages in environment at /home/kskrick/miniconda2/envs/hits:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
bedtools 2.30.0 h7d7f7ad_2 bioconda
bzip2 1.0.8 h7f98852_4 conda-forge
ca-certificates 2022.12.7 ha878542_0 conda-forge
libblas 3.9.0 16_linux64_openblas conda-forge
libcblas 3.9.0 16_linux64_openblas conda-forge
libgcc-ng 12.2.0 h65d4601_19 conda-forge
libgfortran-ng 12.2.0 h69a702a_19 conda-forge
libgfortran5 12.2.0 h337968e_19 conda-forge
libgomp 12.2.0 h65d4601_19 conda-forge
liblapack 3.9.0 16_linux64_openblas conda-forge
libopenblas 0.3.21 pthreads_h78a6416_3 conda-forge
libstdcxx-ng 12.2.0 h46fd767_19 conda-forge
ncurses 5.9 10 conda-forge
numpy 1.19.5 py36hfc0c790_2 conda-forge
openssl 1.0.2u h516909a_0 conda-forge
pandas 1.1.5 py36h284efc9_0 conda-forge
pip 21.3.1 pyhd8ed1ab_0 conda-forge
pybedtools 0.7.10 py36ha92aebf_3 bioconda
pymc 2.3.8 py36h405e7e7_2 conda-forge
pysam 0.8.3 py36h30a8e3e_8 bioconda
python 3.6.3 4 conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python_abi 3.6 2_cp36m conda-forge
pytz 2023.2 pyhd8ed1ab_0 conda-forge
readline 7.0 0 conda-forge
samtools 1.3.1 0 bioconda
scipy 1.5.3 py36h81d768a_1 conda-forge
setuptools 58.0.4 py36h5fab9bb_2 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sqlite 3.20.1 2 conda-forge
tk 8.6.11 h27826a3_1 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
zlib 1.2.11 h36c2ea0_1011 conda-forge