Comments (8)
maringos
commented on May 27, 2024
UPDATE
The pipeline ended successfully, but there were some warnings...
e543d2e41b8f05d35d0397fb4de31534.fasta: Permission denied
e543d2e41b8f05d35d0397fb4de31534.fasta: Permission denied
17e1d8eb0086971abcc54afdee34c56f.fasta: Permission denied
17e1d8eb0086971abcc54afdee34c56f.fasta: Permission denied
7.1.1.5.fasta: Permission denied
7.1.1.5.fasta: Permission denied
1.10.3.12.fasta: Permission denied
1.10.3.12.fasta: Permission denied
cat: /home/minerva/gapseq/src/../dat/seq/Bacteria/unrev/1.10.3.12.fasta: No such file or directory
7.3.2.1.fasta: Permission denied
7.3.2.1.fasta: Permission denied
3.6.3.27.fasta: Permission denied
3.6.3.27.fasta: Permission denied
cat: /home/minerva/gapseq/src/../dat/seq/Bacteria/unrev/3.6.3.27.fasta: No such file or directory
27afa5e63b8aa9a2bb3b88ad8465dd74.fasta: Permission denied
27afa5e63b8aa9a2bb3b88ad8465dd74.fasta: Permission denied
1.1.1.157.fasta: Permission denied
1.1.1.157.fasta: Permission denied
d962345e17c98027bf113de051ac71bb.fasta: Permission denied
d962345e17c98027bf113de051ac71bb.fasta: Permission denied
f6cfe0fda408673f619c00c57a2cbcfe.fasta: Permission denied
f6cfe0fda408673f619c00c57a2cbcfe.fasta: Permission denied
290309402041b41c0de020b01ed41189.fasta: Permission denied
290309402041b41c0de020b01ed41189.fasta: Permission denied
98409a50a1004642d0b281964db53d19.fasta: Permission denied
98409a50a1004642d0b281964db53d19.fasta: Permission denied
b22dcdef3a4303298a5fdb13213a434e.fasta: Permission denied
b22dcdef3a4303298a5fdb13213a434e.fasta: Permission denied
11d790911e1c29cc7c451e6603ed8ba4.fasta: Permission denied
11d790911e1c29cc7c451e6603ed8ba4.fasta: Permission denied
521aedf98c8d875b6a52530815e7e665.fasta: Permission denied
521aedf98c8d875b6a52530815e7e665.fasta: Permission denied
5aa13e240b12a77ce3f98b6abd92cb0a.fasta: Permission denied
5aa13e240b12a77ce3f98b6abd92cb0a.fasta: Permission denied
25cbfc0bc2e9ce7532bfd6db6e5d1d07.fasta: Permission denied
25cbfc0bc2e9ce7532bfd6db6e5d1d07.fasta: Permission denied
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jotech
commented on May 27, 2024
the warning about the duplicate pathway ID is removed from non-verbose runs now!
the permission denied warning is strange and potentially more serious.
Could you report file access rights of one example file (ls -l) and provide the gapseq call?
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maringos
commented on May 27, 2024
For instance... -rw-r--r-- 1 root root 1758 Feb 21 19:35 7.1.1.5.fasta
I think this is related to the fact that my pc did not allow me to install gapseq as normal user, but as root. I will re-run the pipeline as root and I will return the output.
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maringos
commented on May 27, 2024
No errors returned. Obviously there was an access issue, because I installed gapseq as root. Take-home message: If you install gapseq as root, then use it as root
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jotech
commented on May 27, 2024
ok this explains it, but you really shouldn't run gapseq as root! why did you need it for install? Never heard that git clone needs super user rights
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maringos
commented on May 27, 2024
I assume this is an issue if someone combines the apt command and git ones during the install (see main page of the software)
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jotech
commented on May 27, 2024
but there is nothing written on doing all as root :D
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jotech
commented on May 27, 2024
i added a reference to sudo
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