PathoFact issueshttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues2022-10-17T13:56:56+02:00https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/47More cores used than specified2022-10-17T13:56:56+02:00Valentina Galatavalentina.galata@uni.luMore cores used than specifiedOne of the reviewers reported that more CPUs were used than specified; he suspects `SignalP`.One of the reviewers reported that more CPUs were used than specified; he suspects `SignalP`.Paper review - Microbiome - 1https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/34Replace SignalP2021-09-30T14:55:36+02:00Valentina Galatavalentina.galata@uni.luReplace SignalPReplace `SignalP` by a tool
- with same/better functionality
- more flexible license
- which can be installed automatically
- e.g. using `conda`, `git submodule` or by downloading a binary
Or, instead of using one tool, use a combin...Replace `SignalP` by a tool
- with same/better functionality
- more flexible license
- which can be installed automatically
- e.g. using `conda`, `git submodule` or by downloading a binary
Or, instead of using one tool, use a combination of several tools as it is done by [Uniprot](https://www.uniprot.org/help/signal)
*Add suggestions for tools as comments*Paper review - Microbiome - 1https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/72Test workflow and common run fails at RGI step at biopython2021-09-06T12:31:47+02:00Michal ZemanTest workflow and common run fails at RGI step at biopythonHi!
I was testing your software and I wasn't able to pass the test workflow (same problem is in normal workflow).
Data were single WGS genome in separate contigs.
Is it problem of my dependencies or some typo in the code?
Tested syste...Hi!
I was testing your software and I wasn't able to pass the test workflow (same problem is in normal workflow).
Data were single WGS genome in separate contigs.
Is it problem of my dependencies or some typo in the code?
Tested system:
Linux Mint 19.3 Tricia based on Ubuntu 18.04 bionic
conda 4.10.1
python 3.8.3.final.0
although when I have conda environment active
python version is 3.6.4
and biopython 1.78
```
Error in rule run_RGI:
jobid: 46
output: /home/kuskus/ANALYSIS/pathofact/PathoFact_results/PathoFact_intermediate/PathoFact_intermediate/AMR/RGI_results/Cl3778/group_1.RGI.txt
log: /home/kuskus/ANALYSIS/pathofact/PathoFact_results/PathoFact_intermediate/logs/Cl3778/group_1.RGI.log (check log file(s) for error message)
conda-env: /home/kuskus/Software/PathoFact/.snakemake/conda/efe64355
shell:
rgi main --input_sequence /home/kuskus/ANALYSIS/pathofact/PathoFact_results/PathoFact_intermediate/splitted/Cl3778/group_1.fasta --output_file /home/kuskus/ANALYSIS/pathofact/PathoFact_results/PathoFact_intermediate/PathoFact_intermediate/AMR/RGI_results/Cl3778/group_1.RGI --input_type protein --local --clean &> /home/kuskus/ANALYSIS/pathofact/PathoFact_results/PathoFact_intermediate/logs/Cl3778/group_1.RGI.log
(exited with non-zero exit code)
```
Log file contains several lines:
```
Traceback (most recent call last):
File "/home/kuskus/Software/PathoFact/.snakemake/conda/efe64355/bin/rgi", line 2, in <module>
from app.MainBase import MainBase
File "/home/kuskus/Software/PathoFact/.snakemake/conda/efe64355/lib/python3.6/site-packages/app/MainBase.py", line 1, in <module>
from app.settings import *
File "/home/kuskus/Software/PathoFact/.snakemake/conda/efe64355/lib/python3.6/site-packages/app/settings.py", line 7, in <module>
from Bio.Alphabet import generic_dna
File "/home/kuskus/.local/lib/python3.6/site-packages/Bio/Alphabet/__init__.py", line 21, in <module>
"Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the ``molecule_type`` as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information."
ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the ``molecule_type`` as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.
```https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/46Dependency gcc/g++2021-01-12T15:25:35+01:00Valentina Galatavalentina.galata@uni.luDependency gcc/g++A reviewer had to install `gcc/g++`.
Check whether this is really necessary and add to dependencies if required.A reviewer had to install `gcc/g++`.
Check whether this is really necessary and add to dependencies if required.Paper review - Microbiome - 1https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/3DeepARG -- git lsf issue2021-01-12T15:24:52+01:00Valentina Galatavalentina.galata@uni.luDeepARG -- git lsf issueThe issue is described [here](https://bitbucket.org/gusphdproj/deeparg-ss/issues/1/git-lfs-erros-when-cloning-the-repository).
It seems to have no effect on tool execution.The issue is described [here](https://bitbucket.org/gusphdproj/deeparg-ss/issues/1/git-lfs-erros-when-cloning-the-repository).
It seems to have no effect on tool execution.Paper review - Microbiome - 1https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/49Replace SeqKit2020-06-11T15:38:12+02:00Valentina Galatavalentina.galata@uni.luReplace SeqKitReviewers reported issues with `SeqKit`.
Since it is used for FASTA splitting it can be replaced easily.Reviewers reported issues with `SeqKit`.
Since it is used for FASTA splitting it can be replaced easily.Paper review - Microbiome - 1https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/22spring-clean: HMMER2020-04-21T15:21:16+02:00Valentina Galatavalentina.galata@uni.luspring-clean: HMMERDependency: 'HMMER'
* [x] `conda` YAML file
* [x] update path in `config.yaml`
* [x] update rule(s)
Impact: Could affect the results if there are any discrepancies between the versions of any dependency. Therefore
- Confirm version: `3...Dependency: 'HMMER'
* [x] `conda` YAML file
* [x] update path in `config.yaml`
* [x] update rule(s)
Impact: Could affect the results if there are any discrepancies between the versions of any dependency. Therefore
- Confirm version: `3.2.1`spring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/21spring-clean: VirSorter2020-04-21T15:10:53+02:00Valentina Galatavalentina.galata@uni.luspring-clean: VirSorterDependency: `VirSorter`
* [x] `conda` YAML file
* [x] rm dir. in `scripts/`
* [x] rm `git clone` from `set-up.sh`
* [x] update path in `config.yaml`
Impact: Could affect the results if there are any discrepancies between the versions o...Dependency: `VirSorter`
* [x] `conda` YAML file
* [x] rm dir. in `scripts/`
* [x] rm `git clone` from `set-up.sh`
* [x] update path in `config.yaml`
Impact: Could affect the results if there are any discrepancies between the versions of any dependency.
Using `conda` installation (XX) instead of `git` repo (commit `v1.0.6-2-g52a1cd6`).
**NOTE**: [v1.0.6 vs. v1.0.6-2-g52a1cd6](https://github.com/simroux/VirSorter/compare/v1.0.6...v1.0.6-2-g52a1cd6)
--> **not sure** if all changes are non-criticalspring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/20spring-clean: PlasFlow2020-04-21T15:09:05+02:00Valentina Galatavalentina.galata@uni.luspring-clean: PlasFlowDependency: `PlasFlow`
* [x] `conda` YAML file
* [x] rm dir. in `scripts/`
* [x] update path in `config.yaml`
* [x] add YAML to rule(s) calling `PlasFlow`
Impact: Could affect the results if there are any discrepancies between the versi...Dependency: `PlasFlow`
* [x] `conda` YAML file
* [x] rm dir. in `scripts/`
* [x] update path in `config.yaml`
* [x] add YAML to rule(s) calling `PlasFlow`
Impact: Could affect the results if there are any discrepancies between the versions of any dependency.
Using `conda` installation (`plasflow=1.1.0`) instead of `git` repo (commit `v1.1-11-g82e9c75`).
**NOTE**: [release v1.1 vs. v1.1-11-g82e9c75](https://github.com/smaegol/PlasFlow/compare/v1.1...v1.1-11-g82e9c75)
- README update
- changed description of arg parser in `PlasFlow.py`
- no other changes in the code
--> No critical changesspring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/19spring-clean: DeepARG2020-04-21T15:09:05+02:00Valentina Galatavalentina.galata@uni.luspring-clean: DeepARGDependency: `DeepARG`
* [x] `git submodule`
* [x] rm dir. in `scripts/`
* [x] rm `git clone` from `set-up.sh`
* [x] update path in `config.yaml`
* [x] set-up commands: replace path and make `DIAMOND` bin executable
```shell
git lfs ins...Dependency: `DeepARG`
* [x] `git submodule`
* [x] rm dir. in `scripts/`
* [x] rm `git clone` from `set-up.sh`
* [x] update path in `config.yaml`
* [x] set-up commands: replace path and make `DIAMOND` bin executable
```shell
git lfs install # if not already done
git submodule add https://gaarangoa@bitbucket.org/gusphdproj/deeparg-ss.git submodules/deeparg-ss
cd submodules/deeparg-ss/
git checkout 14b8dce
```
Impact: Could affect the results if there are any discrepancies between the versions of any dependency. Therefore:
* Confirm `git` version
* Use same YAML as in original repospring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/17spring-clean: DeepVirFinder2020-04-21T15:09:05+02:00Valentina Galatavalentina.galata@uni.luspring-clean: DeepVirFinderDependency: `DeepVirFinder`
* [x] `git submodule` (for version see below)
* [x] rm dir. in `scripts/`
* [x] rm `git clone` from `set-up.sh`
* [x] update path in `config.yaml`
```shell
git submodule add https://github.com/jessieren/Deep...Dependency: `DeepVirFinder`
* [x] `git submodule` (for version see below)
* [x] rm dir. in `scripts/`
* [x] rm `git clone` from `set-up.sh`
* [x] update path in `config.yaml`
```shell
git submodule add https://github.com/jessieren/DeepVirFinder.git submodules/DeepVirFinder
cd submodules/DeepVirFinder
git checkout ddb4a94
```
Impact: Could affect the results if there are any discrepancies between the versions of any dependency. Therefore:
- Confirm `git` version
- Use same YAML as in original repospring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/16spring-clean: main YAML file2020-04-20T14:18:45+02:00Valentina Galatavalentina.galata@uni.luspring-clean: main YAML fileCreate main `conda` YAML file containing
- `python=3.6.4`
- `snakemake=5.5.4`Create main `conda` YAML file containing
- `python=3.6.4`
- `snakemake=5.5.4`spring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.lu