This repository was archived by the owner on Oct 18, 2024. It is now read-only.
This repository was archived by the owner on Oct 18, 2024. It is now read-only.
Barcode_split on P2solo SQK-RBK114-24 data fails #145
Description
Hi,
: running pycoQC v2.5.2 in a conda env (see list below)
My data was obtained with the current SUP basecalling pipeline on the gridion (guppy 7.1.4 , Super-accurate basecalling, 400 bps).
I could run the pycoQC command on my summary file but fail to run BarcodeSplit.
Can you please help me find out what is wrong here, is this command meant for my data?
Barcode_split -f sequencing_summary_PAK69211_a2c347b0_825e701d.txt.gz -o split_results
Import data from sequencing summary file(s) and cleanup
Read files and import in a dataframe
Check input data files
Parse data files
Merge data
Cleanup missing barcodes values
Cleaning up low frequency barcodes
Split data per barcode
Processing data for Barcode barcode01
Traceback (most recent call last):
File "/opt/miniconda3/envs/pycoqc/bin/Barcode_split", line 10, in <module>
sys.exit(main_Barcode_split())
File "/opt/miniconda3/envs/pycoqc/lib/python3.7/site-packages/pycoQC/__main__.py", line 215, in main_Barcode_split
quiet=args.quiet)
File "/opt/miniconda3/envs/pycoqc/lib/python3.7/site-packages/pycoQC/Barcode_split.py", line 113, in Barcode_split
barcode_df.to_csv(file_name, sep="\t", index=False)
File "/opt/miniconda3/envs/pycoqc/lib/python3.7/site-packages/pandas/core/generic.py", line 3228, in to_csv
formatter.save()
File "/opt/miniconda3/envs/pycoqc/lib/python3.7/site-packages/pandas/io/formats/csvs.py", line 183, in save
compression=self.compression,
File "/opt/miniconda3/envs/pycoqc/lib/python3.7/site-packages/pandas/io/common.py", line 399, in _get_handle
f = open(path_or_buf, mode, encoding=encoding, newline="")
FileNotFoundError: [Errno 2] No such file or directory: 'split_results/sequencing_summary_barcode01.txt'
I also tried to use the only barcode file I found in my data folder with -b
Barcode_split -f sequencing_summary_PAK69211_a2c347b0_825e701d.txt.gz -b barcode_alignment_PAK69211_a2c347b0_825e701d.tsv -o split_results
Import data from sequencing summary file(s) and cleanup
Read files and import in a dataframe
Check input data files
Parse data files
Traceback (most recent call last):
File "/opt/miniconda3/envs/pycoqc/bin/Barcode_split", line 10, in <module>
sys.exit(main_Barcode_split())
File "/opt/miniconda3/envs/pycoqc/lib/python3.7/site-packages/pycoQC/__main__.py", line 215, in main_Barcode_split
quiet=args.quiet)
File "/opt/miniconda3/envs/pycoqc/lib/python3.7/site-packages/pycoQC/Barcode_split.py", line 71, in Barcode_split
pps = pycoQC_parse(summary_file=summary_file, barcode_file=barcode_file, cleanup=False, verbose=verbose, quiet=quiet)
File "/opt/miniconda3/envs/pycoqc/lib/python3.7/site-packages/pycoQC/pycoQC_parse.py", line 97, in __init__
barcode_reads_df = self._parse_barcode()
File "/opt/miniconda3/envs/pycoqc/lib/python3.7/site-packages/pycoQC/pycoQC_parse.py", line 168, in _parse_barcode
raise pycoQCError ("File {} does not contain required barcode information".format(fp))
NameError: name 'fp' is not defined
my conda env: (python 3.7.12, pandas 0.25.1 )
# packages in environment at /opt/miniconda3/envs/pycoqc:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
attrs 22.1.0 py37h06a4308_0
blas 1.0 openblas
brotlipy 0.7.0 py37h27cfd23_1003
bzip2 1.0.8 h7b6447c_0
c-ares 1.19.1 h5eee18b_0
ca-certificates 2023.08.22 h06a4308_0
certifi 2022.12.7 py37h06a4308_0
cffi 1.15.1 py37h5eee18b_3
charset-normalizer 2.0.4 pyhd3eb1b0_0
cryptography 38.0.2 py37h5994e8b_1 conda-forge
curl 8.4.0 hdbd6064_0
decorator 5.1.1 pyhd3eb1b0_0
flit-core 3.6.0 pyhd3eb1b0_0
h5py 2.9.0 py37h7918eee_0
hdf5 1.10.4 hb1b8bf9_0
idna 3.4 py37h06a4308_0
importlib-metadata 4.11.3 py37h06a4308_0
importlib_metadata 4.11.3 hd3eb1b0_0
importlib_resources 5.2.0 pyhd3eb1b0_1
jinja2 2.10.1 py37_0
jsonschema 4.17.3 py37h06a4308_0
jupyter_core 4.11.2 py37h06a4308_0
krb5 1.20.1 h143b758_1
ld_impl_linux-64 2.38 h1181459_1
libblas 3.9.0 13_linux64_openblas conda-forge
libcblas 3.9.0 13_linux64_openblas conda-forge
libcurl 8.4.0 h251f7ec_0
libdeflate 1.3 h516909a_0 conda-forge
libedit 3.1.20221030 h5eee18b_0
libev 4.33 h7f8727e_1
libffi 3.4.4 h6a678d5_0
libgcc-ng 13.2.0 h807b86a_2 conda-forge
libgfortran-ng 7.5.0 ha8ba4b0_17
libgfortran4 7.5.0 ha8ba4b0_17
libgomp 13.2.0 h807b86a_2 conda-forge
liblapack 3.9.0 13_linux64_openblas conda-forge
libnghttp2 1.57.0 h2d74bed_0
libnsl 2.0.0 h5eee18b_0
libopenblas 0.3.18 hf726d26_0
libssh2 1.10.0 hdbd6064_2
libstdcxx-ng 11.2.0 h1234567_1
libzlib 1.2.13 hd590300_5 conda-forge
markupsafe 2.0.1 py37h27cfd23_0
nbformat 5.7.0 py37h06a4308_0
ncurses 6.4 h6a678d5_0
numpy 1.17.1 py37h95a1406_0 conda-forge
openssl 3.0.12 h7f8727e_0
pandas 0.25.1 py37he6710b0_0
pip 22.3.1 py37h06a4308_0
pkgutil-resolve-name 1.3.10 py37h06a4308_0
plotly 4.1.0 py_0 conda-forge
pycoqc 2.5.2 py_0 bioconda
pycparser 2.21 pyhd3eb1b0_0
pyopenssl 23.0.0 py37h06a4308_0
pyrsistent 0.18.0 py37heee7806_0
pysam 0.15.3 py37hbcae180_3 bioconda
pysocks 1.7.1 py37_1
python 3.7.12 hf930737_100_cpython conda-forge
python-dateutil 2.8.2 pyhd3eb1b0_0
python-fastjsonschema 2.16.2 py37h06a4308_0
python_abi 3.7 4_cp37m conda-forge
pytz 2022.7 py37h06a4308_0
readline 8.2 h5eee18b_0
requests 2.28.1 py37h06a4308_0
retrying 1.3.3 pyhd3eb1b0_2
scipy 1.3.1 py37he2b7bc3_0
setuptools 65.6.3 py37h06a4308_0
six 1.16.0 pyhd3eb1b0_1
sqlite 3.41.2 h5eee18b_0
tk 8.6.12 h1ccaba5_0
tqdm 4.35.0 py_0 conda-forge
traitlets 5.7.1 py37h06a4308_0
typing_extensions 4.4.0 py37h06a4308_0
urllib3 1.26.14 py37h06a4308_0
wheel 0.38.4 py37h06a4308_0
xz 5.2.10 h5eee18b_1
zipp 3.11.0 py37h06a4308_0
zlib 1.2.13 hd590300_5 conda-forge