aveglia / vampirus Goto Github PK
View Code? Open in Web Editor NEWAutomated virus amplicon sequencing analysis program integrated with Nextflow pipeline manager.
License: MIT License
vampirus's People
Contributors
Stargazers
Watchers
vampirus's Issues
ggtree error: "Error: object ‘get_aes_var’ is not exported by 'namespace:rvcheck'"
I noticed I was getting an error with ggtree on some systems I set vAMPirus up on. This was caused by a conflict with the ggtree version, rvcheck version and R version selected by conda while building the environment.
Here is how to fix the issue:
After you have built the vAMPirus environment using the .yml file provided:
- Activate vAMPirus environment
conda activate vAMPirus
- Call R
R
- Check if there is a ggtree issue:
library(ggtree)
- If you get "Error: object ‘get_aes_var’ is not exported by 'namespace:rvcheck'" as ouput do:
devtools::install_version('rvcheck',version='0.1.7')
-
Chose a mirror and install the right version of rvcheck needed (v0.1.7) -- for some reason after i selected a mirror I recieved a message saying the package didnt exist, just re-run the command form step 4 and it should install fine.
-
If installation succesful then close out R
q()
- Re-open R and test
R
library(ggtree)
Hopefully this fix works for everyone, please let me know if this does not work for anyone.
Error in DataMask$new(.data, caller_env) : argument "caller_env" is missing, with no default
I noticed I was getting an error with ggtree on some systems I set vAMPirus up on. This was caused by a conflict with the ggtree version, dplyr version and R version selected by conda while building the environment.
Here is how to fix the issue:
After you have built the vAMPirus environment using the .yml file provided:
- Activate vAMPirus environment:
conda activate vAMPirus
- Call R:
R
- We are going to downgrade the dplyr version:
devtools::install_version('dplyr',version='1.0.5')
Chose a mirror and install the right version of dplyr needed (v1.0.5) -- for some reason after i selected a mirror I recieved a message saying the package didnt exist, just re-run the command form step 4 and it should install fine.
If installation succesful then close out R and you should be good to test vAMPirus with the test commands!
Hopefully this fix works for everyone, please let me know if this does not work for anyone.
Error executing process > 'AminoType_Phylogeny'
Help solve the problem, please. I suppose it's about the program modeltest-ng. Since only the portable version was installed. Other versions have the output illegal instruction
Debian 10.
Something went wrong. Check error message below and/or log files.
Error executing process > 'AminoType_Phylogeny'
Caused by:
Process `AminoType_Phylogeny` terminated with an error exit status (2)
Command executed:
# Protein_Alignment
pre=$(echo vAMPirusAnalysis_AminoTypes_noTaxonomy.fasta | awk -F ".fasta" '{print $1}' )
mafft --thread 2 --maxiterate 15000 --auto vAMPirusAnalysis_AminoTypes_noTaxonomy.fasta >${pre}_ALN.fasta
trimal -in ${pre}_ALN.fasta -out ${pre}_aln.fasta -keepheader -fasta -automated1 -htmlout ${pre}_aln.html
# Protein_ModelTest
modeltest-ng -i ${pre}_aln.fasta -p 2 -o ${pre}_mt -d aa -s 203 --disable-checkpoint
# Protein_Phylogeny
if [ "" != "" ];then
iqtree -s ${pre}_aln.fasta --prefix ${pre}_iq --redo -T auto
elif [[ "false" != "false" && "false" != "false" ]];then
mod=$(tail -12 ${pre}_aln.fasta.log | head -1 | awk '{print $6}')
iqtree -s ${pre}_aln.fasta --prefix ${pre}_iq -m ${mod} --redo -nt auto -b 1000
elif [[ "false" != "false" && "false" != "false" ]];then
mod=$(tail -12 ${pre}_aln.fasta.log | head -1 | awk '{print $6}')
iqtree -s ${pre}_aln.fasta --prefix ${pre}_iq -m ${mod} --redo -nt auto -bb 1000 -bnni
elif [ "false" != "false" ];then
iqtree -s ${pre}_aln.fasta --prefix ${pre}_iq -m MFP --redo -nt auto -b 1000
elif [ "false" != "false" ];then
iqtree -s ${pre}_aln.fasta --prefix ${pre}_iq -m MFP --redo -nt auto -bb 1000 -bnni
else
iqtree -s ${pre}_aln.fasta --prefix ${pre}_iq -m MFP --redo -nt auto -bb 1000 -bnni
fi
Command exit status:
2
Command output:
4 RTREV 0 -2999.4129 59788.8257 48.7916 0.0000
5 PMB 0 -3001.4599 59792.9199 52.8857 0.0000
6 JTT-DCMUT 0 -3002.4592 59794.9185 54.8843 0.0000
7 JTT 0 -3003.1980 59796.3959 56.3618 0.0000
8 BLOSUM62 0 -3009.1494 59808.2987 68.2646 0.0000
9 CPREV 0 -3012.6505 59815.3011 75.2669 0.0000
10 DCMUT 0 -3020.6636 59831.3273 91.2931 0.0000
--------------------------------------------------------------------------------
Best model according to AICc
---------------------------
Model: LG
lnL: -2975.0171
Frequencies: 0.0791 0.0559 0.0420 0.0531 0.0129 0.0408 0.0716 0.0573 0.0224 0.0622 0.0991 0.0646 0.0230 0.0423 0.0440 0.0612 0.0533 0.0121 0.0342 0.0691
Inv. sites prop: -
Gamma shape: -
Score: 59740.0342
Weight: 0.9999
---------------------------
Parameter importances
---------------------------
P.Inv: 0.0000
Gamma: 0.0000
Gamma-Inv: 0.0000
Frequencies: -
---------------------------
Model averaged estimates
---------------------------
P.Inv: 0.0000
Alpha: 1.3558
Alpha-P.Inv: 1.3725
P.Inv-Alpha: 0.0000
Frequencies: -
Commands:
> phyml -i vAMPirusAnalysis_AminoTypes_noTaxonomy_aln.fasta -d aa -m LG -f m -v 0 -a 0 -c 1 -o tlr
> raxmlHPC-SSE3 -s vAMPirusAnalysis_AminoTypes_noTaxonomy_aln.fasta -m PROTGAMMALG -n EXEC_NAME -p PARSIMONY_SEED
> raxml-ng --msa vAMPirusAnalysis_AminoTypes_noTaxonomy_aln.fasta --model LG
> paup -s vAMPirusAnalysis_AminoTypes_noTaxonomy_aln.fasta
> iqtree -s vAMPirusAnalysis_AminoTypes_noTaxonomy_aln.fasta -m LG
Summary:
Partition 1/1:
Model Score Weight
----------------------------------------------------------
BIC LG+G4 6500.8375 0.8969
AIC LG+G4 6118.5972 0.7310
AICc LG 59740.0342 0.9999
Execution results written to vAMPirusAnalysis_AminoTypes_noTaxonomy_mt.out
Starting tree written to vAMPirusAnalysis_AminoTypes_noTaxonomy_mt.tree
Command error:
004-0154-0 (thread 1) identical
004-0154-0 (thread 1) worse
004-0155-0 (thread 1) identical
004-0155-0 (thread 1) worse
004-0156-1 (thread 2) identical
004-0156-1 (thread 1) identical
004-0156-1 (thread 1) worse
004-0157-1 (thread 2) worse
004-0158-1 (thread 2) identical
004-0158-1 (thread 2) worse
004-0159-0 (thread 1) identical
004-0159-0 (thread 1) worse
004-0160-0 (thread 2) identical
004-0160-0 (thread 2) worse
004-0161-1 (thread 1) identical
004-0161-1 (thread 1) worse
004-0162-1 (thread 2) identical
004-0162-1 (thread 2) worse
Converged.
Converged2.
done
dvtditr (aa) Version 7.407
alg=A, model=BLOSUM62, 1.53, -0.00, -0.00, noshift, amax=0.0
2 thread(s)
Strategy:
L-INS-i (Probably most accurate, very slow)
Iterative refinement method (<16) with LOCAL pairwise alignment information
If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.
The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.
[error] modeltest-ng: Warning: Substitution schemes will be ignored
Invalid "--prefix" option.
Work dir:
/home/sergey/vAMPirus-1.0.1/work/10/1f1ee7200415d6140fe9e55b229236
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
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.