PathoFact issueshttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues2023-03-18T19:36:31+01:00https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/61error while running run_PLASMID2023-03-18T19:36:31+01:00sabina-llrerror while running run_PLASMIDHi, I am trying to test for the correct installation of PathoFact using the test module. Unfortunately I get this message:
Error in rule run_PLASMID:
jobid: 39
output: test/output_test_again/PathoFact_intermediate/MGE/plasmid/Pl...Hi, I am trying to test for the correct installation of PathoFact using the test module. Unfortunately I get this message:
Error in rule run_PLASMID:
jobid: 39
output: test/output_test_again/PathoFact_intermediate/MGE/plasmid/PlasFlow/test_sample/group_1_plasflow_prediction.tsv
log: test/output_test_again/logs/test_sample/group_1_plasflow_prediction.log (check log file(s) for error message)
conda-env: /net/fs-1/home01/sale/PathoFact/PathoFact/.snakemake/conda/d6afdeea
shell:
PlasFlow.py --input test/output_test_again/PathoFact_intermediate/MGE/plasmid_splitted/test_sample/group_1.fasta --output test/output_test_again/PathoFact_intermediate/MGE/plasmid/PlasFlow/test_sample/group_1_plasflow_prediction.tsv --threshold 0.7 &> test/output_test_again/logs/test_sample/group_1_plasflow_prediction.log
(exited with non-zero exit code)
Do you have any suggestion on how to solve this issue? (log file is attached)
Thanks very much in advance,
Kind Regards,
Sabina
[group_1_plasflow_prediction.log](/uploads/64e74de02a8f5c80f13a8b31f53c5bd0/group_1_plasflow_prediction.log)https://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/59Input: allow to provide a protein FAA file2022-06-15T15:31:24+02:00Valentina Galatavalentina.galata@uni.luInput: allow to provide a protein FAA fileTo be able to include `PathoFact` into other workflows and to use the already existing annotations, it should be allowed to provide a protein FAA file as input (together with the corresponding contigs FASTA).To be able to include `PathoFact` into other workflows and to use the already existing annotations, it should be allowed to provide a protein FAA file as input (together with the corresponding contigs FASTA).https://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/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/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/54Skip prodigal and use curated annotation2022-08-10T15:14:30+02:00avilaHugoSkip prodigal and use curated annotationDear developers,
I have an extensively cured dataset of annotated genomes, but when I run pathofact with fastas files I lose those annotations. Is there a way to use my annotaions to run the program, such as using a gbk or gff file?
(...Dear developers,
I have an extensively cured dataset of annotated genomes, but when I run pathofact with fastas files I lose those annotations. Is there a way to use my annotaions to run the program, such as using a gbk or gff file?
(quick fix if you are a user like me with the same problem: use blast 100% to find match between Prodigal locus tags and your annotations.)https://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/51Update deeparg installation2020-06-18T16:58:08+02:00Laura DeniesUpdate deeparg installationInclude upgraded installation method of deepargInclude upgraded installation method of deeparghttps://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/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/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/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/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/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/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/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/42intallation with docker/singularity2020-06-08T08:15:55+02:00soilmicrobiomeintallation with docker/singularityI am excited to use this program. But I work on a HPC which does not allow for conda. Is it possible to have the program available to pull with docker/singularity?
thanksI am excited to use this program. But I work on a HPC which does not allow for conda. Is it possible to have the program available to pull with docker/singularity?
thankshttps://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 - 1