PathoFact issueshttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues2022-06-01T23:43:08+02:00https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/79Adding information in the final PathoFact report2022-06-01T23:43:08+02:00ntromasAdding information in the final PathoFact reportHi!
I wonder if it would be possible to add some extra information in the PathoFact report, for example AMR database (deepARG or RGI), as this information is already in the AMR report.
Thanks !Hi!
I wonder if it would be possible to add some extra information in the PathoFact report, for example AMR database (deepARG or RGI), as this information is already in the AMR report.
Thanks !https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/50Add Prodigal to Pipeline2020-06-11T15:38:23+02:00Laura DeniesAdd Prodigal to PipelineLaura DeniesLaura Denieshttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/43Add RGI (AMR prediction)2020-06-18T13:23:04+02:00Valentina Galatavalentina.galata@uni.luAdd RGI (AMR prediction)Add `RGI` for AMR prediction
- [paper](https://pubmed.ncbi.nlm.nih.gov/31665441/)
- [repo](https://github.com/arpcard/rgi)
* [x] Evaluate for incorporation
* [x] `conda` YAML file
* [x] relevant parameters in config
* [x] rule to gener...Add `RGI` for AMR prediction
- [paper](https://pubmed.ncbi.nlm.nih.gov/31665441/)
- [repo](https://github.com/arpcard/rgi)
* [x] Evaluate for incorporation
* [x] `conda` YAML file
* [x] relevant parameters in config
* [x] rule to generate predictions
* [x] combine with other resultsPaper review - Microbiome - 1Laura DeniesLaura Denieshttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/62AMR.R2021-04-12T14:22:45+02:00ntromasAMR.RHi, I just got this error and I think it is related to R but not sure. Have you ever met a similar issue?
Error in rule combine_AMR:
jobid: 698
output: /mnt/f92456ad-0760-4f94-b5b5-0b8a862df46a/Pawel/Trimmed/Reads/dRep_wat_das_n...Hi, I just got this error and I think it is related to R but not sure. Have you ever met a similar issue?
Error in rule combine_AMR:
jobid: 698
output: /mnt/f92456ad-0760-4f94-b5b5-0b8a862df46a/Pawel/Trimmed/Reads/dRep_wat_das_new/dereplicated_genomes/genome_edit_name/PathoFact_results_MAGs_wat/PathoFact_intermediate/AMR/MAG-S14_P1C590_AMR_prediction.tsv
log: /mnt/f92456ad-0760-4f94-b5b5-0b8a862df46a/Pawel/Trimmed/Reads/dRep_wat_das_new/dereplicated_genomes/genome_edit_name/PathoFact_results_MAGs_wat/PathoFact_intermediate/logs/MAG-S14_P1C590/combine_AMR_temp.log (check log file(s) for error message)
conda-env: /home/nico/programmes/PathoFact/.snakemake/conda/81817da1
RuleException:
CalledProcessError in line 111 of /home/nico/programmes/PathoFact/rules/AMR/AMR.smk:
Command 'source /home/nico/miniconda3/bin/activate '/home/nico/programmes/PathoFact/.snakemake/conda/81817da1'; set -euo pipefail; Rscript --vanilla /home/nico/programmes/PathoFact/.snakemake/scripts/tmpezv1gqqn.AMR.R' returned non-zero exit status 1.
File "/home/nico/programmes/PathoFact/rules/AMR/AMR.smk", line 111, in __rule_combine_AMR
File "/home/nico/miniconda3/envs/PathoFact/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Here is the log information:
cat /mnt/f92456ad-0760-4f94-b5b5-0b8a862df46a/Pawel/Trimmed/Reads/dRep_wat_das_new/dereplicated_genomes/genome_edit_name/PathoFact_results_MAGs_wat/PathoFact_intermediate/logs/MAG-S14_P1C590/combine_AMR_temp.log
Registered S3 methods overwritten by 'ggplot2':
method from
[.quosures rlang
c.quosures rlang
print.quosures rlang
Registered S3 method overwritten by 'rvest':
method from
read_xml.response xml2
── Attaching packages ─────────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.1.1 ✔ purrr 0.3.2
✔ tibble 2.1.1 ✔ dplyr 0.8.0.1
✔ tidyr 0.8.3 ✔ stringr 1.4.0
✔ readr 1.3.1 ✔ forcats 0.4.0
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()
Error: `f` must be a factor (or character vector or numeric vector).
Execution halted
snakemake -v
5.5.4
Cheers,
NicoValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/65assembled contigs fa files2021-08-28T18:36:09+02:00mhmismassembled contigs fa filesHello,
I have assembled contigs using megahit with the extension of .fa How could I parse them in the PathoFact as it only accepts .fna files?Hello,
I have assembled contigs using megahit with the extension of .fa How could I parse them in the PathoFact as it only accepts .fna files?https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/94CalledProcessError in line 29 of Combine_Toxin_SignalP.smk:2022-09-19T14:59:34+02:00Ghost UserCalledProcessError in line 29 of Combine_Toxin_SignalP.smk:I run PathoFact with ```snakemake -s Snakefile --use-conda --rerun-incomplete --cores 28 -p``` and encountered a CalledProcessError. The run is not interrupted but remains at the current step for two days now (with average CPU usage of 1...I run PathoFact with ```snakemake -s Snakefile --use-conda --rerun-incomplete --cores 28 -p``` and encountered a CalledProcessError. The run is not interrupted but remains at the current step for two days now (with average CPU usage of 15). I have seen another user experiencing a similar issue (https://gitlab.lcsb.uni.lu/laura.denies/PathoFact/-/issues/90) but all my FASTA files contain more than one contig. What effect has the CalledProcessError on the final outcome? Thanks!
```
RuleException:
CalledProcessError in line 29 of /pathofact/PathoFact/rules/Toxin/Combine_Toxin_SignalP.smk:
Command 'source /miniconda3/bin/activate '/pathofact/PathoFact/.snakemake/conda/fb1f3485'; set -euo pipefail; Rscript --vanilla /pathofact/PathoFact/.snakemake/scripts/tmp23lfmhsd.ownHMM_library.R' returned non-zero exit status 1.
File "/protect/pathofact/PathoFact/rules/Toxin/Combine_Toxin_SignalP.smk", line 29, in __rule_R_script
File "/miniconda3/envs/PathoFact/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Removing output files of failed job R_script since they might be corrupted:
/pathofact/contigs_raw_files/PathoFact_results/PathoFact_report/Toxin_gene_library_ABC.tsv
[Sun Jul 24 10:14:54 2022]
Finished job 37616.
31250 of 33263 steps (94%) done
[Sun Jul 24 10:14:58 2022]
Finished job 289.
31251 of 33263 steps (94%) done
```https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/81Cluster documentation2023-02-20T14:57:03+01:00Benjamin WingfieldCluster documentationHello,
I would like to run PathoFact using my local SLURM cluster but it's not clear to me how to run the provided example.
Looking at `cluster.yaml`, I have to modify parameters to match my own cluster. I have edited partition, but I ...Hello,
I would like to run PathoFact using my local SLURM cluster but it's not clear to me how to run the provided example.
Looking at `cluster.yaml`, I have to modify parameters to match my own cluster. I have edited partition, but I don't normally set the `-q` parameter. Can I delete the quality parameter?
Thanks,
Benhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/75CondaVerificationError after installation2021-09-01T13:48:10+02:00AndrewCondaVerificationError after installationHi,
I followed Installation guide step by step. But when I tried to run PathoFact got the error:
<details>
<summary>console output for test from guide</summary>
```bash
(PathoFact) anri@anriPC:/media/anri/FAE8F3E0E8F39959/PathoFact...Hi,
I followed Installation guide step by step. But when I tried to run PathoFact got the error:
<details>
<summary>console output for test from guide</summary>
```bash
(PathoFact) anri@anriPC:/media/anri/FAE8F3E0E8F39959/PathoFact-master$ snakemake -s test/Snakefile --use-conda --reason --cores 4 -p
Building DAG of jobs...
Executing subworkflow pathofact.
Building DAG of jobs...
Creating conda environment envs/VirSorter.yaml...
Downloading remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /media/anri/FAE8F3E0E8F39959/PathoFact-master/rules/AMR/../../envs/VirSorter.yaml:
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
Downloading and Extracting Packages
libcurl-7.69.1 | 573 KB | ########## | 100%
libedit-3.1.20170329 | 172 KB | ########## | 100%
entrez-direct-13.3 | 4.7 MB | ########## | 100%
perl-moose-2.2011 | 444 KB | ########## | 100%
perl-class-method-mo | 13 KB | ########## | 100%
perl-module-implemen | 9 KB | ########## | 100%
perl-mro-compat-0.13 | 10 KB | ########## | 100%
perl-getopt-long-2.5 | 27 KB | ########## | 100%
perl-package-stash-0 | 66 KB | ########## | 100%
perl-sub-name-0.21 | 13 KB | ########## | 100%
perl-apache-test-1.4 | 115 KB | ########## | 100%
perl-package-depreca | 10 KB | ########## | 100%
muscle-3.8.1551 | 280 KB | ########## | 100%
perl-devel-overloadi | 8 KB | ########## | 100%
perl-devel-stacktrac | 16 KB | ########## | 100%
blast-2.9.0 | 17.7 MB | ########## | 100%
perl-sub-install-0.9 | 10 KB | ########## | 100%
perl-yaml-1.29 | 41 KB | ########## | 100%
perl-moo-2.003004 | 38 KB | ########## | 100%
ncurses-6.1 | 1.3 MB | ########## | 100%
perl-params-util-1.0 | 14 KB | ########## | 100%
perl-role-tiny-2.000 | 15 KB | ########## | 100%
mcl-14.137 | 2.2 MB | ########## | 100%
perl-package-stash-x | 21 KB | ########## | 100%
perl-dist-checkconfl | 10 KB | ########## | 100%
perl-eval-closure-0. | 11 KB | ########## | 100%
libssh2-1.8.2 | 257 KB | ########## | 100%
metagene_annotator-1 | 729 KB | ########## | 100%
curl-7.69.1 | 137 KB | ########## | 100%
perl-sub-exporter-pr | 8 KB | ########## | 100%
perl-file-which-1.23 | 12 KB | ########## | 100%
perl-devel-globaldes | 7 KB | ########## | 100%
krb5-1.17.1 | 1.5 MB | ########## | 100%
perl-class-load-0.25 | 12 KB | ########## | 100%
perl-module-runtime- | 7 KB | ########## | 100%
virsorter-1.0.5 | 47 KB | ########## | 100%
perl-bioperl-1.6.924 | 2.2 MB | ########## | 100%
perl-class-load-xs-0 | 13 KB | ########## | 100%
perl-module-runtime- | 15 KB | ########## | 100%
perl-sub-quote-2.006 | 18 KB | ########## | 100%
diamond-0.9.14 | 556 KB | ########## | 100%
perl-sub-exporter-0. | 30 KB | ########## | 100%
perl-parallel-forkma | 21 KB | ########## | 100%
perl-sub-identify-0. | 12 KB | ########## | 100%
openssl-1.1.1f | 2.1 MB | ########## | 100%
perl-data-optlist-0. | 10 KB | ########## | 100%
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
ERROR conda.core.link:_execute(699): An error occurred while installing package 'conda-forge::perl-5.26.2-h516909a_1006'.
Rolling back transaction: ...working... done
[Errno 22] Invalid argument: '/media/anri/FAE8F3E0E8F39959/PathoFact-master/.snakemake/conda/f8c49d3c/man/man3/App::Cpan.3'
()
```
</details>
<details>
<summary>console output for my data</summary>
```bash
anri@anriPC:/media/anri/FAE8F3E0E8F39959/PathoFact-master$ conda activate PathoFact
(PathoFact) anri@anriPC:/media/anri/FAE8F3E0E8F39959/PathoFact-master$ snakemake -s Snakefile --use-conda --reason --cores 4 -p
Building DAG of jobs...
Creating conda environment envs/Biopython.yaml...
Downloading remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /media/anri/FAE8F3E0E8F39959/PathoFact-master/rules/Universal/../../envs/Biopython.yaml:
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... failed
CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/data/boston_house_prices.csv'
specified in the package manifest cannot be found.
CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/data/breast_cancer.csv'
specified in the package manifest cannot be found.
CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/data/iris.csv'
specified in the package manifest cannot be found.
CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/data/linnerud_exercise.csv'
specified in the package manifest cannot be found.
CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/data/linnerud_physiological.csv'
specified in the package manifest cannot be found.
CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/data/wine_data.csv'
specified in the package manifest cannot be found.
CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/descr/boston_house_prices.rst'
specified in the package manifest cannot be found.
CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/descr/breast_cancer.rst'
specified in the package manifest cannot be found.
CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/descr/california_housing.rst'
specified in the package manifest cannot be found.
CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/descr/covtype.rst'
specified in the package manifest cannot be found.
CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/descr/diabetes.rst'
specified in the package manifest cannot be found.
CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/descr/digits.rst'
specified in the package manifest cannot be found.
CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/descr/iris.rst'
specified in the package manifest cannot be found.
CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/descr/kddcup99.rst'
specified in the package manifest cannot be found.
CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/descr/lfw.rst'
specified in the package manifest cannot be found.
CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/descr/linnerud.rst'
specified in the package manifest cannot be found.
CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/descr/olivetti_faces.rst'
specified in the package manifest cannot be found.
CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/descr/rcv1.rst'
specified in the package manifest cannot be found.
CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/descr/twenty_newsgroups.rst'
specified in the package manifest cannot be found.
CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/descr/wine_data.rst'
specified in the package manifest cannot be found.
CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/images/china.jpg'
specified in the package manifest cannot be found.
CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/images/flower.jpg'
specified in the package manifest cannot be found.
SafetyError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/neighbors/ball_tree.cpython-36m-x86_64-linux-gnu.so'
has an incorrect size.
reported size: 538712 bytes
actual size: 241152 bytes
CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/utils/sparsefuncs_fast.cpython-36m-x86_64-linux-gnu.so'
specified in the package manifest cannot be found.
```
</details>
Whats wrong?https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/69Config file config.yaml not found2021-08-31T15:58:07+02:00Owenke247Config file config.yaml not found**Script:**
snakemake -s /proj/spteds/spted00/software/PathoFact/Snakefile --use-conda --cores 1 --configfile /proj/spteds/spted00/software/PathoFact/configfile.yaml
**Error report:**
WorkflowError in line 3 of /proj/spteds/spted00/so...**Script:**
snakemake -s /proj/spteds/spted00/software/PathoFact/Snakefile --use-conda --cores 1 --configfile /proj/spteds/spted00/software/PathoFact/configfile.yaml
**Error report:**
WorkflowError in line 3 of /proj/spteds/spted00/software/PathoFact/Snakefile:
Config file config.yaml not found.
File "/proj/spteds/spted00/software/PathoFact/Snakefile", line 3, in <module>
**configfile.yaml**:
pathofact:
sample: ["M.036","R3.099"] # requires user input
project: "PathoFact_res" # requires user input
datadir: "/proj/spteds/spted00/Project/CDI/pathfact/contig" # requires user input
workflow: "complete" #options: "complete", "AMR", "Tox", "Vir"
size_fasta: 10000 #Adjustable to preference
scripts: "scripts"
signalp: "/proj/spteds/spted00/software/PathoFact/signalP/signalp-5.0b/bin" # requires user input
deepvirfinder: "submodules/DeepVirFinder/dvf.py"
tox_hmm: "databases/toxins/combined_Toxin.hmm"
tox_lib: "databases/library_HMM_Toxins.csv"
tox_threshold: 40 #Bitscore threshold of the toxin prediction, adjustable by user to preference
vir_hmm: "databases/virulence/Virulence_factor.hmm"
vir_domains: "databases/models_and_domains"
plasflow_threshold: 0.7
plasflow_minlen: 1000
runtime:
short: "00:10:00"
medium: "01:00:00"
long: "02:00:00"
mem:
normal_mem_per_core_gb: "4G"
big_mem_cores: 4
big_mem_per_core_gb: "30G"
Your comments will be much appreciated.https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/100Convert PathoFact AMR_MGE_report.tsv output to GFF2023-04-14T09:18:45+02:00theadrijaConvert PathoFact AMR_MGE_report.tsv output to GFFIs there any way I can convert the .tsv report of AMR_MGE to GFF?Is there any way I can convert the .tsv report of AMR_MGE to GFF?https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/98Could not create conda environment from VirSorter.yaml2023-02-21T14:52:22+01:00thr44pw00dCould not create conda environment from VirSorter.yamlHi,
I installed PathoFact as described in README.md and tried to run the test module using the command:
`snakemake -s test/Snakefile --use-conda --reason --cores 1 -p`
Unfortunately it failed to create the conda environment "envs/VirSor...Hi,
I installed PathoFact as described in README.md and tried to run the test module using the command:
`snakemake -s test/Snakefile --use-conda --reason --cores 1 -p`
Unfortunately it failed to create the conda environment "envs/VirSorter.yaml". Attached the output to the terminal after I issued the snakemake command. If I understand correctly it's mostly about conflicts regarding perl.
Would you have a suggestion how to resolve this?
Thanks in advance!
[stdout.txt](/uploads/4f1f7958e1225bc55db45af9a622c84e/stdout.txt)https://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/44DeepARG - parameters in config file2020-06-22T11:26:03+02:00Valentina Galatavalentina.galata@uni.luDeepARG - parameters in config fileAdd relevant parameters to config fileAdd relevant parameters to config filePaper review - Microbiome - 1https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/56DeepVirFinder: Resource unavailable2021-01-21T09:09:49+01:00Susheel BusiDeepVirFinder: Resource unavailable- During the `AMR` module, every once a while a sample fails for `DeepVirFinder` due to a `numpy` error
- This error only occurs on certain HPC clusters, example: at UL - only fails on `esb-compute-01` and not on `IRIS`
- Specific error ...- During the `AMR` module, every once a while a sample fails for `DeepVirFinder` due to a `numpy` error
- This error only occurs on certain HPC clusters, example: at UL - only fails on `esb-compute-01` and not on `IRIS`
- Specific error message: `Resource unavailable`Laura DeniesLaura Denieshttps://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/41Documentation2021-01-12T15:25:21+01:00Valentina Galatavalentina.galata@uni.luDocumentation
* [x] output files
* [x] config file
* [x] running time and memory requirements
* [x] output files
* [x] config file
* [x] running time and memory requirementsPaper review - Microbiome - 1https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/96DVF using all cores2023-02-19T16:58:20+01:00Ella KantorDVF using all coresHi,
I have been running PathoFact successfully but I noticed that the steps that run dvf.py are taking up all available cores on my workstation even though I specified 12. I found an issue similar to this #47 which is closed now but I d...Hi,
I have been running PathoFact successfully but I noticed that the steps that run dvf.py are taking up all available cores on my workstation even though I specified 12. I found an issue similar to this #47 which is closed now but I don't see if there is a fix for it, maybe something I could change in that dvf.py script? I looked into it and it was my understanding that DVF is limited to 4 by default.
I am running AMR only with the modified AMR_MGE.R script that you gave to Nico in issue #93 which seems to be taking much longer now than with the buggy script (I assume that is a good sign that it is working).
Hopefully there is a change that I could make to leave some cores free to the fellow users on the workstation.
Thank you,
Ellahttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/60erorr while running classifier and run_Virifinder2021-08-28T18:37:55+02:00AA8898erorr while running classifier and run_VirifinderI get the following error message while running PathoFact on the test data
```
bad escape \s at position 0
Traceback (most recent call last):
File "/opt/miniconda3/lib/python3.7/sre_parse.py", line 1015, in parse_template
this = ch...I get the following error message while running PathoFact on the test data
```
bad escape \s at position 0
Traceback (most recent call last):
File "/opt/miniconda3/lib/python3.7/sre_parse.py", line 1015, in parse_template
this = chr(ESCAPES[this][1])
KeyError: '\\s'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "scripts/virulence_prediction.py", line 4, in <module>
import pandas as pd
File "/opt/miniconda3/lib/python3.7/site-packages/pandas/__init__.py", line 6, in <module>
from . import hashtable, tslib, lib
File "pandas/tslib.pyx", line 3222, in init pandas.tslib
File "pandas/tslib.pyx", line 3169, in pandas.tslib.TimeRE.__init__
File "pandas/tslib.pyx", line 3206, in pandas.tslib.TimeRE.pattern
File "/opt/miniconda3/lib/python3.7/re.py", line 309, in _subx
template = _compile_repl(template, pattern)
File "/opt/miniconda3/lib/python3.7/re.py", line 300, in _compile_repl
return sre_parse.parse_template(repl, pattern)
File "/opt/miniconda3/lib/python3.7/sre_parse.py", line 1018, in parse_template
raise s.error('bad escape %s' % this, len(this))
re.error: bad escape \s at position 0
```
how can I resolve this? thankshttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/39Error if no VirSorter results in AMR_MGE.R2021-03-24T16:26:45+01:00Valentina Galatavalentina.galata@uni.luError if no VirSorter results in AMR_MGE.RIf `VirSorter` does not have any results then the script `AMR_MGE.R` fails with an error:
```
Error: `f` must be a factor (or character vector or numeric vector).
```
This happens here:
```R
Phage_prediction$VirSorter_prediction <- fct...If `VirSorter` does not have any results then the script `AMR_MGE.R` fails with an error:
```
Error: `f` must be a factor (or character vector or numeric vector).
```
This happens here:
```R
Phage_prediction$VirSorter_prediction <- fct_explicit_na(Phage_prediction$VirSorter_prediction, na_level = "-")
```
Reason: `Phage_prediction$VirSorter_prediction` contains only `NA`s.Paper review - Microbiome - 1Valentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/66Error in Combine_Toxin_SignalP.smk file2021-04-12T14:42:05+02:00Vadim (Dani) DubinskyError in Combine_Toxin_SignalP.smk fileDear developer,
When I try to run the tool with the standard command (snakemake -s PathoFact/Snakefile --use-conda --reason --cores 4 –p) I got the following error:
> MissingInputException in line 11 of /home/danid/PathoFact/rules/Toxin...Dear developer,
When I try to run the tool with the standard command (snakemake -s PathoFact/Snakefile --use-conda --reason --cores 4 –p) I got the following error:
> MissingInputException in line 11 of /home/danid/PathoFact/rules/Toxin/Combine_Toxin_SignalP.smk:
>
> Missing input files for rule R_script:
>
> databases/library_HMM_Toxins.csv
I installed PathoFact with Conda, set up the config.yml file, and all the libraries seem to be in place, including the library_HMM_Toxins.csv appearing in the error.
I will appreciate your help,
Best
Vadim