PathoFact issueshttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues2021-08-28T18:36:09+02:00https://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/57PathoFact for assembled genomes2021-08-28T18:35:29+02:00in3skaPathoFact for assembled genomes![Bildschirmfoto_2021-01-31_um_17.06.22](/uploads/94e465e6aaffb58786232492933e2111/Bildschirmfoto_2021-01-31_um_17.06.22.jpg)Hello @laura.denies,
I have a similar question regarding the issue "PathoFact for metagenome assembled genomes (...![Bildschirmfoto_2021-01-31_um_17.06.22](/uploads/94e465e6aaffb58786232492933e2111/Bildschirmfoto_2021-01-31_um_17.06.22.jpg)Hello @laura.denies,
I have a similar question regarding the issue "PathoFact for metagenome assembled genomes (MAGs)". In my case, I have the WGS of a bacterial isolate that is closed and was obtained by Hybrid assembly via Unicycler. I guess that my input is a bit too big for the pipeline, cause I always get the following error message (see picture above).
Do you have any suggestions?
Regardshttps://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
Vadimhttps://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/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/58how to deal if i am not allowed to create conda environment on my server?2021-03-08T14:46:03+01:00AA8898how to deal if i am not allowed to create conda environment on my server?I am currently trying to run PathoFact on my server but I am not allowed to creare conda environment so it give me back this error:
```
Could not create conda environment from /home/PathoFact/rules/AMR/../../envs/Biopython.yaml:
Collect...I am currently trying to run PathoFact on my server but I am not allowed to creare conda environment so it give me back this error:
```
Could not create conda environment from /home/PathoFact/rules/AMR/../../envs/Biopython.yaml:
Collecting package metadata (repodata.json): ...working... failed
NotWritableError: The current user does not have write permissions to a required path.
path: /opt/miniconda3/pkgs/cache/497deca9.json
```
Is there a way to overcome this issue and so run the pipeline without being sudoer?
Thanks a lothttps://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/55SyntaxError in line 85, Preprocessing.smk2021-01-20T11:40:04+01:00Ghost UserSyntaxError in line 85, Preprocessing.smkHey,
I have read the PathoFact publication. Very impressing, thank you very much! I have tried to install and test the tool with my own data, but I always get stuck in the initial run (also with the test run).
I get the following error ...Hey,
I have read the PathoFact publication. Very impressing, thank you very much! I have tried to install and test the tool with my own data, but I always get stuck in the initial run (also with the test run).
I get the following error message: <br>
SyntaxError in line 85 of /PathoFact/rules/Universal/Preprocessing.smk: <br>
invalid syntax <br>
File "/PathoFact/Snakefile", line 8, in \<module> <br>
File "/PathoFact/workflows/Combine_PathoFact_workflow.smk", line 3, in \<module> <br>
<br>
Any ideas on how I can fix the problem? <br>
Thank you very much in advance! <br>
<br>
Mariehttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/52Signal IP version2021-01-12T15:26:20+01:00Adrian-HowardSignal IP versionHello as I have seen in the Dependencies SignalIP is needed and saids that the version is 5.0 but then it asks to download version 4.1g. Just wanted to make sure with version is needed to use PathoFact.Hello as I have seen in the Dependencies SignalIP is needed and saids that the version is 5.0 but then it asks to download version 4.1g. Just wanted to make sure with version is needed to use PathoFact.https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/40PlasFlow minimal contig length from config2021-01-12T15:25:57+01:00Valentina Galatavalentina.galata@uni.luPlasFlow minimal contig length from configGet the minimal contig length for `PlasFlow` from the config file: rule `filter_seq` in `Plasmid.smk`.Get the minimal contig length for `PlasFlow` from the config file: rule `filter_seq` in `Plasmid.smk`.Paper review - Microbiome - 1https://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/37PlasFlow threshold from config2021-01-12T15:25:03+01:00Valentina Galatavalentina.galata@uni.luPlasFlow threshold from configGet the parameter `threshold` for `PlasFlow` from the config file.Get the parameter `threshold` for `PlasFlow` from the config file.Paper review - Microbiome - 1Valentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://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/36README.md update2021-01-12T15:24:45+01:00Valentina Galatavalentina.galata@uni.luREADME.md update* [x] move "Pipeline environment" below "PathoFact"
- the env. can only be created after the repo has been cloned
* [x] remove `-b SpringClean` from the CMD for cloning the repo
* [x] in "Input files" there are two `SAMPLE_A.fna`: re...* [x] move "Pipeline environment" below "PathoFact"
- the env. can only be created after the repo has been cloned
* [x] remove `-b SpringClean` from the CMD for cloning the repo
* [x] in "Input files" there are two `SAMPLE_A.fna`: replace one with `SAMPLE_A.faa`Paper review - Microbiome - 1https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/27Snakemake rule messages2020-08-06T12:06:37+02:00Valentina Galatavalentina.galata@uni.luSnakemake rule messagesAdd a short message to each `snakemake` rule
Impact: Will not affect the pipelineAdd a short message to each `snakemake` rule
Impact: Will not affect the pipelinePaper review - Microbiome - 1Laura DeniesLaura Denieshttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/45Reduce output size2020-06-22T14:40:26+02:00Valentina Galatavalentina.galata@uni.luReduce output sizeRemove all intermediate files which are not relevant to the user.
Files with relevant results should be compressed, e.g. output created by `PlasFlow`.
Check if there are very large log files.
* [x] make not relevant intermediate files t...Remove all intermediate files which are not relevant to the user.
Files with relevant results should be compressed, e.g. output created by `PlasFlow`.
Check if there are very large log files.
* [x] make not relevant intermediate files temporary w/ `temp(...)`
* [ ] redirect `hmmer`s stdout to `/dev/null` instead of the log file
* [ ] compress relevant intermediate files
* [x] add rule to removes files which cannot be made temp() (files used in snakemake checkpoints) Paper review - Microbiome - 1Laura DeniesLaura Denieshttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/48Output format2020-06-22T13:37:43+02:00Valentina Galatavalentina.galata@uni.luOutput formatUse consistent output format
* [x] Either `TSV` or `CSV`, not both
* [x] Labels: `pathogenic`, `non-pathogenic` etc.Use consistent output format
* [x] Either `TSV` or `CSV`, not both
* [x] Labels: `pathogenic`, `non-pathogenic` etc.Paper review - Microbiome - 1Laura DeniesLaura Denieshttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/35Update SignalP2020-06-22T11:26:19+02:00Valentina Galatavalentina.galata@uni.luUpdate SignalPConsider using version `5.0b` instead of `4.X`.
See the list of available versions [here](https://services.healthtech.dtu.dk/software.php).
Related to issue #34: no need for an update if `SignalP` will be replaced by a different tool.Consider using version `5.0b` instead of `4.X`.
See the list of available versions [here](https://services.healthtech.dtu.dk/software.php).
Related to issue #34: no need for an update if `SignalP` will be replaced by a different tool.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 - 1