Comments (8)
AllisonStander
commented on August 22, 2024
2
Thank you so much for the help! I got it working!
from alitv-perl-interface.
iimog
commented on August 22, 2024
from alitv-perl-interface.
iimog
commented on August 22, 2024
I created a docker container now, you can try it for your dataset with:
docker run --rm -u $UID:$GID -v $PWD:/data alitv/alitv:markus Nicotiana_tabacumA.fasta Nicotiana_tabacumB.fasta
from alitv-perl-interface.
AllisonStander
commented on August 22, 2024
Good day,
I am having the same issue:
FATAL - Unable to load alignment module 'AliTV::Alignment::lastz' at /home/allison/Programs/AliTV/AliTV-perl-interface/bin/../lib/AliTV/Script.pm line 123.
Unable to load alignment module 'AliTV::Alignment::lastz' at /home/allison/Programs/AliTV/AliTV-perl-interface/bin/../lib/AliTV/Script.pm line 123.
I am unsure how to use the docker container to fix this issue? I am not familiar with docker.
Regards,
Allison
from alitv-perl-interface.
iimog
commented on August 22, 2024
Hi Allison,
we still don't know what causes this error for some users. We can try to finally identify the root of this issue. As this might take some time, and probably some trial and error here is how you can use docker to run AliTV:
docker run --rm -u $UID:$GID -v $PWD:/data alitv/alitv:markus my_file.yml
This assumes that my_file.yml is your yml file and is located in the folder you are running docker in. All files mentioned in there (e.g. fasta and feature files) are in this directory (or subdirectories) as well. Let me know if that already works for you or if you want to dig deeper to solve the original issue.
Best,
Markus
from alitv-perl-interface.
AllisonStander
commented on August 22, 2024
Hi Markus,
So I created the yml file using
./alitv.pl --project Rooibos_Chloroplast --output test --overwrite /home/allison/Documents/00_Internship/00_Chloroplast/00_GetOrganelle/Rooibos_Chloroplast_repeatpattern1.fasta /home/allison/Documents/00_Internship/00_Chloroplast/10_Legume_Ch-Genomes/*fasta
The output yml file is:
alignment:
parameter:
- --format=maf
- --noytrim
- --ambiguous=iupac
- --gapped
- --strand=both
program: lastz
genomes:
- name: /home/allison/Documents/00_Internship/00_Chloroplast/00_GetOrganelle/Rooibos_Chloroplast_repeatpattern1.fasta
sequence_files:
- /home/allison/Documents/00_Internship/00_Chloroplast/00_GetOrganelle/Rooibos_Chloroplast_repeatpattern1.fasta
- name: /home/allison/Documents/00_Internship/00_Chloroplast/10_Legume_Ch-Genomes/Crotalaria_pallida_chloroplast_MT920364.1.fasta
sequence_files:
- /home/allison/Documents/00_Internship/00_Chloroplast/10_Legume_Ch-Genomes/Crotalaria_pallida_chloroplast_MT920364.1.fasta
- name: /home/allison/Documents/00_Internship/00_Chloroplast/10_Legume_Ch-Genomes/Glycine_max_NC_007942.1.fasta
sequence_files:
- /home/allison/Documents/00_Internship/00_Chloroplast/10_Legume_Ch-Genomes/Glycine_max_NC_007942.1.fasta
- name: /home/allison/Documents/00_Internship/00_Chloroplast/10_Legume_Ch-Genomes/Lotus_japonicus_chloroplast_NC_002694.1.fasta
sequence_files:
- /home/allison/Documents/00_Internship/00_Chloroplast/10_Legume_Ch-Genomes/Lotus_japonicus_chloroplast_NC_002694.1.fasta
- name: /home/allison/Documents/00_Internship/00_Chloroplast/10_Legume_Ch-Genomes/Lupinus_albus_NC_026681.1.fasta
sequence_files:
- /home/allison/Documents/00_Internship/00_Chloroplast/10_Legume_Ch-Genomes/Lupinus_albus_NC_026681.1.fasta
- name: /home/allison/Documents/00_Internship/00_Chloroplast/10_Legume_Ch-Genomes/Lupinus_atlanticus_KU726827.1.fasta
sequence_files:
- /home/allison/Documents/00_Internship/00_Chloroplast/10_Legume_Ch-Genomes/Lupinus_atlanticus_KU726827.1.fasta
- name: /home/allison/Documents/00_Internship/00_Chloroplast/10_Legume_Ch-Genomes/Maackia_floribunda_KX388160.1.fasta
sequence_files:
- /home/allison/Documents/00_Internship/00_Chloroplast/10_Legume_Ch-Genomes/Maackia_floribunda_KX388160.1.fasta
- name: /home/allison/Documents/00_Internship/00_Chloroplast/10_Legume_Ch-Genomes/Medicago_trancatula_NC_003119.8.fasta
sequence_files:
- /home/allison/Documents/00_Internship/00_Chloroplast/10_Legume_Ch-Genomes/Medicago_trancatula_NC_003119.8.fasta
- name: /home/allison/Documents/00_Internship/00_Chloroplast/10_Legume_Ch-Genomes/Ormosia_hosiei_NC_039418.1.fasta
sequence_files:
- /home/allison/Documents/00_Internship/00_Chloroplast/10_Legume_Ch-Genomes/Ormosia_hosiei_NC_039418.1.fasta
- name: /home/allison/Documents/00_Internship/00_Chloroplast/10_Legume_Ch-Genomes/Ormosi_boluoensis_chloroplast_MN886968.1.fasta
sequence_files:
- /home/allison/Documents/00_Internship/00_Chloroplast/10_Legume_Ch-Genomes/Ormosi_boluoensis_chloroplast_MN886968.1.fasta
- name: /home/allison/Documents/00_Internship/00_Chloroplast/10_Legume_Ch-Genomes/Sophora_tonkinensis_NC_042688.1.fasta
sequence_files:
- /home/allison/Documents/00_Internship/00_Chloroplast/10_Legume_Ch-Genomes/Sophora_tonkinensis_NC_042688.1.fasta
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
When I run
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sudo docker run --rm -u $UID:$GID -v $PWD:/data alitv/alitv:markus ./Rooibos_Chloroplast.yml
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
I get the following:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/home/allison/Documents/00_Internship/00_Chloroplast/00_GetOrganelle/Rooibos_Chloroplast_repeatpattern1.fasta': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl/5.26.1/Bio/Root/Root.pm:449
STACK: Bio::Root::IO::_initialize_io /usr/local/share/perl/5.26.1/Bio/Root/IO.pm:272
STACK: Bio::SeqIO::_initialize /usr/local/share/perl/5.26.1/Bio/SeqIO.pm:508
STACK: Bio::SeqIO::fasta::_initialize /usr/local/share/perl/5.26.1/Bio/SeqIO/fasta.pm:88
STACK: Bio::SeqIO::new /usr/local/share/perl/5.26.1/Bio/SeqIO.pm:384
STACK: Bio::SeqIO::new /usr/local/share/perl/5.26.1/Bio/SeqIO.pm:430
STACK: AliTV::Genome::_initialize /AliTV-perl-interface/bin/../lib/AliTV/Genome.pm:59
STACK: AliTV::Base::new /AliTV-perl-interface/bin/../lib/AliTV/Base.pm:18
STACK: AliTV::_import_genomes /AliTV-perl-interface/bin/../lib/AliTV.pm:481
STACK: AliTV::run /AliTV-perl-interface/bin/../lib/AliTV.pm:70
STACK: AliTV::Script::run /AliTV-perl-interface/bin/../lib/AliTV/Script.pm:123
STACK: /AliTV-perl-interface/bin/alitv.pl:11
The file and folder
/home/allison/Documents/00_Internship/00_Chloroplast/00_GetOrganelle/Rooibos_Chloroplast_repeatpattern1.fasta does exist, and contains no typos.
Any idea how I can fix this?
from alitv-perl-interface.
iimog
commented on August 22, 2024
Yes, the problem is with the absolute paths. When using docker you don't see the same filesystem inside the container as you have outside. The -v $PWD:/data part of the command mounts your current working directory to the /data directory inside the container (this is the default working directory inside the container). So if you use relative paths (relative to the working directory you run docker from) instead of absolute paths it should work.
from alitv-perl-interface.
greatfireball
commented on August 22, 2024
Thanks for your help @iimog
from alitv-perl-interface.
Related Issues (20)
- Remove output section from default YAML file
- Re-add the `--self` option
- Unable to load alignment module HOT 5
- Running alitv.pl twice with overwrite results in an error HOT 1
- Add `--no-self` option
- Support lastz Sequence Specifiers HOT 3
- Add lastz binary
- Different rounding of identity in links and filters HOT 3
- Add option to just create yml
- Default lastz parameter --ambiguous=iupac HOT 5
- Add default lastz option --allocate:traceback=800M HOT 1
- Add CITATION.cff
- reduce the number of alignment HOT 3
- can't download AliTV onto mac HOT 5
- unable to identify sequence in sequence set by name HOT 12
- Buggy BioPerl warning too verbose HOT 2
- Unable to find lastz HOT 2
- Demo annotation occurred in my own json file. HOT 8
- MSG: Failed validation of sequence '[unidentified sequence]'. Invalid characters were: _900108945113131010000441 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 alitv-perl-interface.