alvis1113
commented
1 year ago In lib/parmsa.py Line 20
from msa_process = subprocess.Popen("clustalw2 -quicktree -quiet -infile=" + msafile)
to msa_process = subprocess.Popen("clustalw2 -quicktree -quiet -infile=" + msafile, shell=True)
this works for me.
Hi， Thanks for developing this user-friendly tool. I installed the software on the basis of your guidline. When i run "phython3 probedesign.py" . Type "human、input_human_genes.txt、20、20、65、75”，Then， An error occured: Number of probes per gene (skip by pressing Enter): <class 'FileNotFoundError'> Traceback (most recent call last): File "probedesign.py", line 18, in
checkinput.getdesigninput()
File "/home/zero/multi_padlock_design-2.1/lib/checkinput.py", line 222, in getdesigninput
headers, basepos, sequences, msa, nocommon = retrieveseq.findseq(genes, hits, outdir_temp)
File "/home/zero/multi_padlock_design-2.1/lib/retrieveseq.py", line 101, in findseq
tempout = parmsa.continuemsa(dirname, msa)
File "/home/zero/multi_padlock_design-2.1/lib/parmsa.py", line 113, in continuemsa
runningmsa(dirname, msa)
File "/home/zero/multi_padlock_design-2.1/lib/parmsa.py", line 105, in runningmsa
runmsa(msafile)
File "/home/zero/multi_padlock_design-2.1/lib/parmsa.py", line 19, in runmsa
msa_process = subprocess.Popen("clustalw2 -quicktree -quiet -infile=" + msafile)
File "/home/zero/miniconda3/lib/python3.8/subprocess.py", line 854, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File "/home/zero/miniconda3/lib/python3.8/subprocess.py", line 1702, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'clustalw2 -quicktree -quiet infile=out/TempFolder20201214175938/PDGFRA_variants.fasta'
I'm looking forward to your reply.