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EEscuderoL opened this issue May 9, 2025 · 0 comments
Open

funannotate iprscan local producing empty XML file #1106

EEscuderoL opened this issue May 9, 2025 · 0 comments

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@EEscuderoL
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Hello! While running interproscan locally:
funannotate iprscan -i predictions/predict_results/Elsinoe_persea.proteins.fa
-m local -o out_iprscan/persea.XML
--iprscan_path /home/efrain.escudero/bin/miniforge3/envs/funannotate/bin/interproscan.sh -c 64

It writes an XML in the output directory, however, it's empty. Outside directory "predictions", a folder appears containing temporary files (proteins). Phobius and SignalP are installed and recognised.

Logfile:
Running InterProScan5 on 7917 proteins
Important: you need to manually configure your interproscan.properties file for embedded workers.
Will try to launch 64 interproscan processes, adjust -c,--cpus for your system
Progress: 8 complete, 0 failed, 0 remaining
Traceback (most recent call last):
File "/home/efrain.escudero/bin/miniforge3/envs/funannotate/lib/python3.9/site-packages/funannotate/aux_scripts/iprscan-local.py", line 409, in
shutil.rmtree(tmpdir)
File "/home/efrain.escudero/bin/miniforge3/envs/funannotate/lib/python3.9/shutil.py", line 734, in rmtree
_rmtree_safe_fd(fd, path, onerror)
File "/home/efrain.escudero/bin/miniforge3/envs/funannotate/lib/python3.9/shutil.py", line 667, in _rmtree_safe_fd
_rmtree_safe_fd(dirfd, fullname, onerror)
File "/home/efrain.escudero/bin/miniforge3/envs/funannotate/lib/python3.9/shutil.py", line 667, in _rmtree_safe_fd
_rmtree_safe_fd(dirfd, fullname, onerror)
File "/home/efrain.escudero/bin/miniforge3/envs/funannotate/lib/python3.9/shutil.py", line 673, in _rmtree_safe_fd
onerror(os.rmdir, fullname, sys.exc_info())
File "/home/efrain.escudero/bin/miniforge3/envs/funannotate/lib/python3.9/shutil.py", line 671, in _rmtree_safe_fd
os.rmdir(entry.name, dir_fd=topfd)
OSError: [Errno 39] Directory not empty: 'jobPanther'

Running in HPC with Red Hat Enterprise Linux 8.6

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