Open naturepoker opened 6 months ago
Quick follow up:
I tested out fresh PhiSpy installations across two separate machines running the same OS (Ubuntu 22.04 LTS), running same commands on conda-installed PhiSpy environments.
Curiously, the command worked perfectly fine on one of the machines, and didn't on the other. Here's the PhiSpy command used:
phispy -o GCF_AccessionNumber_Species_Taxon --color --phmms ~/phrogs.hmm --threads 2 GCF_AccessionNumber_Species_Taxon.gbk
Base python version (OS) across the two machines are same: 3.10.12 PhiSpy environment (conda) python version across the two machines are the same as well: 3.10.13
However, base conda python version across both machines are difference - Conda base python version for the machine with successful run: 3.11.5 Conda base python version for the machine with failed run: 3.12.1
Another note - even on the machine that completed a successful run, trying to run a looped command over a directory of genbank files like:
for f in *.gbk; do n=$(basename $f .gbk); phispy -o $n --color --phmms ~/phrogs.hmm --threads 2 $f; done
Results in failure even when addressing the same file. Overall whether PhiSpy is going to work on a given file on a given machine or not had been pretty unpredictable...
Editing to add that the issue is definitely with result writing portion of the PhiSpy process. After trimming input file names I get terminal stdout results indicating the pipeline has run normally, but the process terminates at the writing step with below error:
Creating output files
Traceback (most recent call last):
File "/home/miniconda3/envs/phispy/bin/phispy", line 10, in <module>
sys.exit(run())
File "/home/miniconda3/envs/phispy/lib/python3.10/site-packages/PhiSpyModules/main.py", line 122, in run
main(sys.argv)
File "/home/miniconda3/envs/phispy/lib/python3.10/site-packages/PhiSpyModules/main.py", line 114, in main
PhiSpyModules.write_all_outputs(**vars(args_parser))
File "/home/miniconda3/envs/phispy/lib/python3.10/site-packages/PhiSpyModules/writers.py", line 325, in write_all_outputs
self.record.get_entry(self.pp[i]['contig']).append_feature(SeqFeature(
TypeError: SeqFeature.__init__() got an unexpected keyword argument 'strand'
At the end the tmp directory with data is deleted (in some cases, not all), leaving only the log file.
Quick follow up:
I tested out fresh PhiSpy installations across two separate machines running the same OS (Ubuntu 22.04 LTS), running same commands on conda-installed PhiSpy environments.
Curiously, the command worked perfectly fine on one of the machines, and didn't on the other. Here's the PhiSpy command used:
phispy -o GCF_AccessionNumber_Species_Taxon --color --phmms ~/phrogs.hmm --threads 2 GCF_AccessionNumber_Species_Taxon.gbk
Base python version (OS) across the two machines are same: 3.10.12 PhiSpy environment (conda) python version across the two machines are the same as well: 3.10.13
However, base conda python version across both machines are difference - Conda base python version for the machine with successful run: 3.11.5 Conda base python version for the machine with failed run: 3.12.1
Another note - even on the machine that completed a successful run, trying to run a looped command over a directory of genbank files like:
for f in *.gbk; do n=$(basename $f .gbk); phispy -o $n --color --phmms ~/phrogs.hmm --threads 2 $f; done
Results in failure even when addressing the same file. Overall whether PhiSpy is going to work on a given file on a given machine or not had been pretty unpredictable...
Editing to add that the issue is definitely with result writing portion of the PhiSpy process. After trimming input file names I get terminal stdout results indicating the pipeline has run normally, but the process terminates at the writing step with below error:
Creating output files Traceback (most recent call last): File "/home/miniconda3/envs/phispy/bin/phispy", line 10, in <module> sys.exit(run()) File "/home/miniconda3/envs/phispy/lib/python3.10/site-packages/PhiSpyModules/main.py", line 122, in run main(sys.argv) File "/home/miniconda3/envs/phispy/lib/python3.10/site-packages/PhiSpyModules/main.py", line 114, in main PhiSpyModules.write_all_outputs(**vars(args_parser)) File "/home/miniconda3/envs/phispy/lib/python3.10/site-packages/PhiSpyModules/writers.py", line 325, in write_all_outputs self.record.get_entry(self.pp[i]['contig']).append_feature(SeqFeature( TypeError: SeqFeature.__init__() got an unexpected keyword argument 'strand'
At the end the tmp directory with data is deleted (in some cases, not all), leaving only the log file.
Hey there, I was experiencing the same issue you had on your last run (TypeError: SeqFeature.__init__() got an unexpected keyword argument 'strand'
) in my conda environment with PhiSpy. It looks like it's an issue with BioPython version 1.82 (https://github.com/biopython/biopython/issues/4563) so after downgrading to 1.81 it ran smoothly.
Hello,
PhisPy process errors out and doesn't produce results file - confirmed same behavior on both separate venv & pip installation and conda environment installation.
Attaching error message (this one specifically from venv installation:
My old lab note shows the same version of PhiSpy (4.2.21) working without issues around 2022. What could have changed since then?
Please feel free to let me know if you need additional data/assistance (alas I'm no good with python). Thank you!