Comments (8)
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
from gapseq.
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?
from gapseq.
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.
from gapseq.
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
from gapseq.
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
from gapseq.
I assume this is an issue if someone combines the apt command and git ones during the install (see main page of the software)
from gapseq.
but there is nothing written on doing all as root :D
from gapseq.
i added a reference to sudo
from gapseq.
Related Issues (20)
- Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached: [rest.uniprot.org] SSL connection timeout HOT 4
- Issue with options when calling subcommand for "gapseq doall". HOT 3
- Download sequences fails HOT 2
- HTML entities for special characters in reaction name causes incorrect uniprot queries HOT 1
- libsbml and libglpk not found while installed using conda HOT 4
- Question: GapSeq includes a protein as being present when it got a bad blast? HOT 14
- Reaction inferred from pseudogene regions when using gapseq on genome fasta file.
- CHNOSZ NOT FOUND HOT 1
- [Request Update] [Tutorial] For anyone who intend to use CPLEX in gapseq HOT 3
- Diamond not used for the transport-find command HOT 2
- Could not use find-transport function using '-m' option for specific metabolite. HOT 8
- subex.tbl issue HOT 1
- Any plans on updating MetaCyc database? HOT 2
- Using seed reaction database in Adapt function HOT 8
- adding pathways| Error: No model reactions found and Error: Error in !opt$sbml.no.output : invalid argument type HOT 6
- Inquiry on instllation HOT 2
- Inquiry on error HOT 5
- Missing exchange reactions are not being added in the "adapt" module HOT 3
- Seawater and related media HOT 1
- Possible inconsistencies in pathway completeness percentages. HOT 2
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from gapseq.