Problem with running Ultraplex #53
Description
Hello,
THanks for developing a potentially incredibly useful tool!
I am new to ultraplex and am trying to run your testdata including barcodes from GitHub. I noticed also that the testdata *.fq.gz seems to contain mainly Ns. When I run Ultraplex with the test data, it throws this error:
ultraplex -i HAL169A1-A22_S1_L001_R1_001.fastq.gz -b barcodes_ultraplex_format.csv -t 10 -dbr --ignore_no_match
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Namespace(adapter='AGATCGGAAGAGCACACGTCTGAA', adapter2='AGATCGGAAGAGCGTCGTG', barcodes='barcodes_ultraplex_format.csv', directory='', dont_build_reference=True, final_min_length=20, fiveprimemismatches=0, ignore_no_match=True, ignore_space_warning=False, input_2='', inputfastq='HAL169A1-A22_S1_L001_R1_001.fastq.gz', keep_barcode=False, min_trim=3, outputprefix='demux', phredquality=30, phredquality_5_prime=0, sbatchcompression=False, threads=10, three_prime_only=False, threeprimemismatches=0, tso_seq='', ultra=False)
Demultiplexing...
Process WorkerProcess-1:
Traceback (most recent call last):
File "/home/admin/anaconda3/envs/ultraplex/lib/python3.8/site-packages/multiprocess/process.py", line 315, in _bootstrap
self.run()
File "/home/admin/anaconda3/envs/ultraplex/lib/python3.8/site-packages/ultraplex/main.py", line 974, in run
new_dict = merge_defaultdicts(prev_dict, read_number)
File "/home/admin/anaconda3/envs/ultraplex/lib/python3.8/site-packages/ultraplex/main.py", line 28, in merge_defaultdicts
merged[key] += value
TypeError: unsupported operand type(s) for +=: 'int' and 'NoneType'
##########
When I interrupt the program, I get this output: "Demultiplexing complete! 165308 reads processed" (rest below). But there is no output.
###########
Traceback (most recent call last):
File "/home/admin/anaconda3/envs/ultraplex/bin/ultraplex", line 11, in
sys.exit(main())
File "/home/admin/anaconda3/envs/ultraplex/lib/python3.8/site-packages/ultraplex/main.py", line 2068, in main
reads_samps_Dict = read_number.get()
File "/home/admin/anaconda3/envs/ultraplex/lib/python3.8/site-packages/multiprocess/queues.py", line 100, in get
res = self._recv_bytes()
File "/home/admin/anaconda3/envs/ultraplex/lib/python3.8/site-packages/multiprocess/connection.py", line 219, in recv_bytes
buf = self._recv_bytes(maxlength)
File "/home/admin/anaconda3/envs/ultraplex/lib/python3.8/site-packages/multiprocess/connection.py", line 417, in _recv_bytes
buf = self._recv(4)
File "/home/admin/anaconda3/envs/ultraplex/lib/python3.8/site-packages/multiprocess/connection.py", line 382, in _recv
chunk = read(handle, remaining)
KeyboardInterrupt
##########
Python version: 3.8, installed in its own Anaconda environment. I also tried to install ultraplex in a fresh Anaconda environment using python 3.7 and 3.9; same problem. I tried installing through mamba with different python versions - same problem.
I got the same error when trying my own data for the various ultraplex installs, so it's not just the test dataset. Now I have no clue how to proceed to get the program to work.
Do you have a suggestion what to do?
Thank you !!
Below are the package versions in my current ultraplex conda environment, just in case this might help:
packages in environment at /home/werthadmin/anaconda3/envs/ultraplex:
Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
ca-certificates 2022.9.24 ha878542_0 conda-forge
cffi 1.15.1 py38h4a40e3a_2 conda-forge
dill 0.3.6 pyhd8ed1ab_1 conda-forge
dnaio 1.2.0 py38he5da3d1_0 bioconda
isa-l 2.30.0 ha770c72_4 conda-forge
ld_impl_linux-64 2.39 hc81fddc_0 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 12.2.0 h65d4601_19 conda-forge
libgomp 12.2.0 h65d4601_19 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libsqlite 3.40.0 h753d276_0 conda-forge
libstdcxx-ng 12.2.0 h46fd767_19 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libzlib 1.2.13 h166bdaf_4 conda-forge
multiprocess 0.70.14 py38h0a891b7_3 conda-forge
ncurses 6.3 h27087fc_1 conda-forge
openssl 3.0.7 h166bdaf_0 conda-forge
packaging 21.3 pyhd8ed1ab_0 conda-forge
pbzip2 1.1.13 0 conda-forge
pigz 2.6 h27826a3_0 conda-forge
pip 22.3.1 pyhd8ed1ab_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge
python 3.8.13 ha86cf86_0_cpython conda-forge
python-isal 1.1.0 py38h0a891b7_1 conda-forge
python_abi 3.8 2_cp38 conda-forge
readline 8.1.2 h0f457ee_0 conda-forge
setuptools 65.5.1 pyhd8ed1ab_0 conda-forge
setuptools-scm 8.0.4 py38h06a4308_0
setuptools_scm 8.0.4 hd3eb1b0_0
sqlite 3.40.0 h4ff8645_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
typing-extensions 4.4.0 hd8ed1ab_0 conda-forge
typing_extensions 4.4.0 pyha770c72_0 conda-forge
ultraplex 1.2.9 py38he5da3d1_1 bioconda
wheel 0.38.4 pyhd8ed1ab_0 conda-forge
xopen 1.7.0 py38h578d9bd_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
zlib 1.2.13 h166bdaf_4 conda-forge
zstandard 0.19.0 py38h0a891b7_0 conda-forge
zstd 1.5.2 h6239696_4 conda-forge