PathoFact issueshttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues2023-09-13T10:12:25+02:00https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/91Error in rule CTDT:2023-09-13T10:12:25+02:00fconstanciasError in rule CTDT:Dear PathoFact developers,
Thanks for your effort developping this very usefull tool.
Could you clarify the different branches (`orf_coinf`, `orf`, `PathoFact_v`, `master` ...)
?
I am using PathoFact using already annotated contigs i....Dear PathoFact developers,
Thanks for your effort developping this very usefull tool.
Could you clarify the different branches (`orf_coinf`, `orf`, `PathoFact_v`, `master` ...)
?
I am using PathoFact using already annotated contigs i.e., ORFs `https://gitlab.lcsb.uni.lu/laura.denies/PathoFact/-/tree/orf_coinf` and I prepared the necessary files: .fna .faa .contig using the script: https://raw.githubusercontent.com/fconstancias/NRP72-FBT/master/functions/prepare_faa_fna_PAthoFact_orf.Rscript.R
I am using the enclosed [config.yaml](/uploads/6bab28ae40b5b022704a7bd305167531/config.yaml)
I run the pipeline using `snakemake -s Snakefile --use-conda --reason --cores 10 -p --configfile analyses/config.yaml`
everything went smooth until the following error:
```
[Fri Jul 1 16:05:57 2022]
Finished job 321.
277 of 1075 steps (26%) done
[Fri Jul 1 16:05:57 2022]
Job 324: Identify features (CTDT) on the following sample(s): PathoFact_results - chicken1_l10000
Reason: Missing output files: /datadrive05/Flo/tools/orf_coinf/analyses/PathoFact_results/PathoFact_intermediate/VIRULENCE/classifier_virulence/chicken1_l10000/group_22_CTDT.txt
python scripts/CTDT.py --file /datadrive05/Flo/tools/orf_coinf/analyses/PathoFact_results/splitted/chicken1_l10000/group_22.fasta --out /datadrive05/Flo/tools/orf_coinf/analyses/PathoFact_results/PathoFact_intermediate/VIRULENCE/classifier_virulence/chicken1_l10000/group_22_CTDT.txt &> /datadrive05/Flo/tools/orf_coinf/analyses/PathoFact_results/logs/chicken1_l10000/group_22_CTDT.log
Activating conda environment: /datadrive05/Flo/tools/orf_coinf/.snakemake/conda/67994cc8
Activating conda environment: /datadrive05/Flo/tools/orf_coinf/.snakemake/conda/67994cc8
[Fri Jul 1 16:05:59 2022]
Error in rule CTDT:
jobid: 319
output: /datadrive05/Flo/tools/orf_coinf/analyses/PathoFact_results/PathoFact_intermediate/VIRULENCE/classifier_virulence/chicken1_l10000/group_6_CTDT.txt
log: /datadrive05/Flo/tools/orf_coinf/analyses/PathoFact_results/logs/chicken1_l10000/group_6_CTDT.log (check log file(s) for error message)
conda-env: /datadrive05/Flo/tools/orf_coinf/.snakemake/conda/67994cc8
shell:
python scripts/CTDT.py --file /datadrive05/Flo/tools/orf_coinf/analyses/PathoFact_results/splitted/chicken1_l10000/group_6.fasta --out /datadrive05/Flo/tools/orf_coinf/analyses/PathoFact_results/PathoFact_intermediate/VIRULENCE/classifier_virulence/chicken1_l10000/group_6_CTDT.txt &> /datadrive05/Flo/tools/orf_coinf/analyses/PathoFact_results/logs/chicken1_l10000/group_6_CTDT.log
(exited with non-zero exit code)
Removing temporary output file /datadrive05/Flo/tools/orf_coinf/analyses/PathoFact_results/PathoFact_intermediate/VIRULENCE/classifier_virulence/chicken1_l10000/group_49_matrix.tsv.
[Fri Jul 1 16:06:00 2022]
Finished job 66.
```
Please find enclosed the logs: [2022-07-01T155547.324708.snakemake.log](/uploads/2142c321b536feddf05ad97afc16537c/2022-07-01T155547.324708.snakemake.log) [group_6_CTDT.log](/uploads/f415d5ad31b6e24516751a131e2001bc/group_6_CTDT.log) as well as the [group_6.fasta.gz](/uploads/e507e6dd8e0187f3d67195b07a4bcad7/group_6.fasta.gz)
```
conda --version
conda 4.12.0
```
[environment.yml](/uploads/bac774322dc73e9f67996ebf53b26f01/environment.yml)
It seems specific to the `VIR` workflow since `AMR` and `Tox` worked fine on the same dataset.
Thanks for the support!https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/101Error in rule run_VirSorter2023-05-28T23:22:25+02:00siva-sagarError in rule run_VirSorterPathofact was actually work fine yesterday but while i started running today i came across this error and unable to proceed forward. there is an issue on this but it is not much of a help.
![error1](/uploads/e38ad746d31c3ac0c8577d82c614...Pathofact was actually work fine yesterday but while i started running today i came across this error and unable to proceed forward. there is an issue on this but it is not much of a help.
![error1](/uploads/e38ad746d31c3ac0c8577d82c6147232/error1.png)
I used these command: snakemake -s Snakefile --use-conda --reason --cores 128 -p
These are the .snakemake log files
[2023-05-23T152917.975027.snakemake.log](/uploads/9d0aa2d4fb70b2fb4d28cf1f6f18aabb/2023-05-23T152917.975027.snakemake.log)
[2023-05-23T150043.964282.snakemake.log](/uploads/1dd537aa971a658eea2374655ac8c271/2023-05-23T150043.964282.snakemake.log)
thank you.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/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/97trouble creating conda env VirSorter.yaml2023-02-21T14:52:22+01:00melinarosytrouble creating conda env VirSorter.yamlHi
I tried to use PathoFact. I installed all requirements. I tried to tun test module but I run into conflict that your current version is 2.31 and it should be 2.17. I paste the last sentences because the eoor is kind of long
- feature...Hi
I tried to use PathoFact. I installed all requirements. I tried to tun test module but I run into conflict that your current version is 2.31 and it should be 2.17. I paste the last sentences because the eoor is kind of long
- feature:/linux-64::__glibc==2.31=0
- feature:|@/linux-64::__glibc==2.31=0
- blast==2.9.0=pl526h3066fca_4 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- bzip2==1.0.8=h516909a_2 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- curl==7.69.1=h33f0ec9_0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- diamond==0.9.14=hd28b015_2 -> libgcc-ng[version='>=4.9'] -> __glibc[version='>=2.17']
- expat==2.2.9=he1b5a44_2 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- krb5==1.17.1=h2fd8d38_0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- libcurl==7.69.1=hf7181ac_0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- libedit==3.1.20170329=hf8c457e_1001 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- libgcc==7.2.0=h69d50b8_2 -> libgcc-ng[version='>=7.2.0'] -> __glibc[version='>=2.17']
- libssh2==1.8.2=h22169c7_2 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- mcl==14.137=pl526h516909a_5 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- metagene_annotator==1.0=h516909a_3 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- muscle==3.8.1551=hc9558a2_5 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- ncurses==6.1=hf484d3e_1002 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- openssl==1.1.1f=h516909a_0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- pcre==8.44=he1b5a44_0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-class-load-xs==0.10=pl526h6bb024c_2 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-compress-raw-bzip2==2.087=pl526he1b5a44_0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-compress-raw-zlib==2.087=pl526hc9558a2_0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-eval-closure==0.14=pl526h6bb024c_4 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-html-parser==3.72=pl526h6bb024c_5 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-io-compress==2.087=pl526he1b5a44_0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-json-xs==2.34=pl526h6bb024c_3 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-moose==2.2011=pl526hf484d3e_1 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-net-ssleay==1.88=pl526h90d6eec_0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-package-stash-xs==0.28=pl526hf484d3e_1 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-package-stash==0.38=pl526hf484d3e_1 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-params-util==1.07=pl526h6bb024c_4 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-pathtools==3.75=pl526h14c3975_1 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-scalar-list-utils==1.52=pl526h516909a_0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-storable==3.15=pl526h14c3975_0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-sub-identify==0.14=pl526h14c3975_0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-xml-parser==2.44_01=pl526ha1d75be_1002 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl==5.26.2=h516909a_1006 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- tk==8.6.10=hed695b0_0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- virsorter==1.0.5=pl526h516909a_4 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- zlib==1.2.11=h516909a_1006 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
Your installed version is: 2.31
could you help me please?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/95Error in rule run_deepARG2023-02-20T14:59:08+01:00WoCer2019Error in rule run_deepARGThanks for the nice tool!
Recently I was running PathoFact with the test data. However, I was confronted with an error shown as follows (group_1.out.mapping.ARG.log).
```
Traceback (most recent call last):
File "/data/LJ/software/patho...Thanks for the nice tool!
Recently I was running PathoFact with the test data. However, I was confronted with an error shown as follows (group_1.out.mapping.ARG.log).
```
Traceback (most recent call last):
File "/data/LJ/software/pathofact/PathoFact/.snakemake/conda/a3c12cf1/bin/deeparg", line 5, in <module>
from deeparg.entry import main
File "/data/LJ/software/pathofact/PathoFact/.snakemake/conda/a3c12cf1/lib/python2.7/site-packages/deeparg/entry.py", line 9, in <module>
import deeparg.predict.bin.deepARG as clf
File "/data/LJ/software/pathofact/PathoFact/.snakemake/conda/a3c12cf1/lib/python2.7/site-packages/deeparg/predict/bin/deepARG.py", line 12, in <module>
from lasagne import layers
File "/data/LJ/software/pathofact/PathoFact/.snakemake/conda/a3c12cf1/lib/python2.7/site-packages/lasagne/__init__.py", line 13, in <module>
""")
ImportError: Could not import Theano.
Please make sure you install a recent enough version of Theano. See
section 'Install from PyPI' in the installation docs for more details:
http://lasagne.readthedocs.org/en/latest/user/installation.html#install-from-pypi
```
Thank you in advance.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/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/89Error in rule SignalPN_aggregate2023-02-19T16:53:40+01:00Gaoyang LuoError in rule SignalPN_aggregate[patho_PW_5M.e286138](/uploads/c0a3f7ef7619079c67529bc9614a5eff/patho_PW_5M.e286138)
Dera @laura.denies
I confronted the issue and I thought it could be the issue of `cat` command line. I don't know why there would be no error when the ...[patho_PW_5M.e286138](/uploads/c0a3f7ef7619079c67529bc9614a5eff/patho_PW_5M.e286138)
Dera @laura.denies
I confronted the issue and I thought it could be the issue of `cat` command line. I don't know why there would be no error when the number of files is small. I don't know if i try "for i in {input}; do cat ${i} >> {output}" will workhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/99Issue from pathofact test2023-02-19T16:39:43+01:00gyudaeIssue from pathofact testHello, im graduate student from South Korea.
I have some problem with installing PathoFact.
After following the instructions, i did test command which was 'snakemake -s test/Snakefile --use-conda --reason --cores 50 -p' to check install....Hello, im graduate student from South Korea.
I have some problem with installing PathoFact.
After following the instructions, i did test command which was 'snakemake -s test/Snakefile --use-conda --reason --cores 50 -p' to check install.
But the following error massage was presented...
Does anyone know this error massage...? I cant figure it out for 1 week...
Package perl-eval-closure conflicts for:
perl-moo==2.003004=pl526_0 -> perl-moose -> perl-eval-closure[version='0.14.*|>=0.04']
perl-eval-closure==0.14=pl526h6bb024c_4
perl-moose==2.2011=pl526hf484d3e_1 -> perl-eval-closure[version='>=0.04']The following specifications were found to be incompatible with your system:
- feature:/linux-64::__glibc==2.35=0
- feature:|@/linux-64::__glibc==2.35=0
- blast==2.9.0=pl526h3066fca_4 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- bzip2==1.0.8=h516909a_2 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- curl==7.69.1=h33f0ec9_0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- diamond==0.9.14=hd28b015_2 -> libgcc-ng[version='>=4.9'] -> __glibc[version='>=2.17']
- expat==2.2.9=he1b5a44_2 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- krb5==1.17.1=h2fd8d38_0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- libcurl==7.69.1=hf7181ac_0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- libedit==3.1.20170329=hf8c457e_1001 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- libgcc==7.2.0=h69d50b8_2 -> libgcc-ng[version='>=7.2.0'] -> __glibc[version='>=2.17']
- libssh2==1.8.2=h22169c7_2 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- mcl==14.137=pl526h516909a_5 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- metagene_annotator==1.0=h516909a_3 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- muscle==3.8.1551=hc9558a2_5 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- ncurses==6.1=hf484d3e_1002 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- openssl==1.1.1f=h516909a_0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- pcre==8.44=he1b5a44_0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-class-load-xs==0.10=pl526h6bb024c_2 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-compress-raw-bzip2==2.087=pl526he1b5a44_0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-compress-raw-zlib==2.087=pl526hc9558a2_0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-eval-closure==0.14=pl526h6bb024c_4 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-html-parser==3.72=pl526h6bb024c_5 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-io-compress==2.087=pl526he1b5a44_0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-json-xs==2.34=pl526h6bb024c_3 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-moose==2.2011=pl526hf484d3e_1 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-net-ssleay==1.88=pl526h90d6eec_0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-package-stash-xs==0.28=pl526hf484d3e_1 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-package-stash==0.38=pl526hf484d3e_1 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-params-util==1.07=pl526h6bb024c_4 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-pathtools==3.75=pl526h14c3975_1 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-scalar-list-utils==1.52=pl526h516909a_0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-storable==3.15=pl526h14c3975_0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-sub-identify==0.14=pl526h14c3975_0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl-xml-parser==2.44_01=pl526ha1d75be_1002 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- perl==5.26.2=h516909a_1006 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- tk==8.6.10=hed695b0_0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- virsorter==1.0.5=pl526h516909a_4 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- zlib==1.2.11=h516909a_1006 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
Your installed version is: 2.35
This is log file of test command. [2023-02-10T110040.706099.snakemake.log](/uploads/9ab917029126f02cbaf650dc217bae6f/2023-02-10T110040.706099.snakemake.log)
Thanks!
GyuDae Leehttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/93NA in MGE prediction2022-10-17T13:56:57+02:00ntromasNA in MGE predictionHi PathoFact team,
I run PathoFact using AMR in the workflow and the run ended without error. However, the AMR report is composed of NA (only NA) in the MGE prediction column. My guess is that there is an issue with the AMR_MGE.R script...Hi PathoFact team,
I run PathoFact using AMR in the workflow and the run ended without error. However, the AMR report is composed of NA (only NA) in the MGE prediction column. My guess is that there is an issue with the AMR_MGE.R script. I used the last version so not sure why I got this. DvF and VirSorter worked properly, same for PlasFlow.
Thanks for the help,
Nicohttps://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/87Error in rule SignalPN_aggregate2022-10-14T15:28:35+02:00Ella KantorError in rule SignalPN_aggregateHello,
I am running a large file and I got this error:
<details><summary>Click to expand</summary>
`[Tue Apr 5 20:11:45 2022]
Error in rule SignalPN_aggregate:
jobid: 289
output: /data2/ekantor/Argal/PathoFact_results_Argal/Pa...Hello,
I am running a large file and I got this error:
<details><summary>Click to expand</summary>
`[Tue Apr 5 20:11:45 2022]
Error in rule SignalPN_aggregate:
jobid: 289
output: /data2/ekantor/Argal/PathoFact_results_Argal/PathoFact_intermediate/SignalP/contigs_Argal/gramn_summary.signalp5
shell:
cat /data2/ekantor/Argal/PathoFact_results_Argal/PathoFact_intermediate/SignalP/Gram-/contigs_Argal/group_1_summary.signalp5 /data2/ekantor/Argal/PathoFact_results_Argal/PathoFact_intermediate/SignalP/Gram-/contigs_Argal/group_2_summary.signalp5`
Then there is a whole list of files that ends with:
`/data2/ekantor/Argal/PathoFact_results_Argal/PathoFact_intermediate/SignalP/Gram-/contigs_Argal/group_3087_summary.signalp5 > /data2/ekantor/Argal/PathoFact_results_Argal/PathoFact_intermediate/SignalP/contigs_Argal/gramn_summary.signalp5
(exited with non-zero exit code)
[Tue Apr 5 20:11:55 2022]
Finished job 3376.
13147 of 14486 steps (91%) done
[Tue Apr 5 20:12:03 2022]
Finished job 2839.
13148 of 14486 steps (91%) done
[Tue Apr 5 20:14:28 2022]
Finished job 206.
13149 of 14486 steps (91%) done`
</details>
There is no log file yet as it is still running, but there hasn't been any progress since that last message.
Here is the full output so far: [nohup.out.zip](/uploads/0e0ffab9013443a7472d6c8b356f3538/nohup.out.zip)
This is the second time I have tried this and the last time I got a similar error but it was:
<details><summary>Click to expand</summary>
`[Fri Apr 1 05:13:24 2022]
Error in rule SignalPP_aggregate:
jobid: 1644
output: /data2/ekantor/Argal/PathoFact_results_Argal/PathoFact_intermediate/SignalP/contigs_Argal/gramp_summary.signalp5
shell:
cat /data2/ekantor/Argal/PathoFact_results_Argal/PathoFact_intermediate/SignalP/Gram+/contigs_Argal/group_1_summary.signalp5...
/data2/ekantor/Argal/PathoFact_results_Argal/PathoFact_intermediate/SignalP/Gram+/contigs_Argal/group_3087_summary.signalp5 > /data2/ekantor/Argal/PathoFact_results_Argal/PathoFact_intermediate/SignalP/contigs_Argal/gramp_summary.signalp5
(exited with non-zero exit code)
[Fri Apr 1 05:13:25 2022]
Finished job 7819.
13271 of 14604 steps (91%) done
[Fri Apr 1 05:15:16 2022]
Finished job 124.
13272 of 14604 steps (91%) done`
</details>
Again, it stopped after that message and there was no progress for a few days. I force killed the program after that but I do not have the log file anymore unfortunately. I reinstalled PathoFact afterwards and ran the test successfully before trying again.
I am running conda version 4.11.0. I installed snakemake newest version 7.3.4 via mamba from the installation instructions on the snakemake docs.
I used 12 cores for the most recent run and 10 cores for the one before it. Could this have something to do with the size of the file?
Thank you,
Ellahttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/83Finished NCBI genomes and PathoFact2022-09-21T07:04:47+02:00vkisandFinished NCBI genomes and PathoFactHi,
I have used the PathoFact successfully on my onw WGSs' containing several contigs. However, now I wanted to test it on finished genomes of similar strains downloaded from NCBI. Whitespaces are deleted from names, but "complete" run f...Hi,
I have used the PathoFact successfully on my onw WGSs' containing several contigs. However, now I wanted to test it on finished genomes of similar strains downloaded from NCBI. Whitespaces are deleted from names, but "complete" run freezes, I would say rather randomly. Re-runs may continue a bit but still never finish. "Vir" or "Tox" were finished, but "AMR" froze too
Any ideas? I increased mem setting a bit
mem:
normal_mem_per_core_gb: "4G"
big_mem_cores: 12
big_mem_per_core_gb: "64G"
cheers,
/vhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/88testing module fails deepARG- how to update deepARG within PathoFact?2022-09-19T15:23:39+02:00RahilRydertesting module fails deepARG- how to update deepARG within PathoFact?Im having the same issue as issue #64 and the solution was to update deepARG 1.0.2 in bitbucket. I am using Ubuntu to run PathoFact. I tried updating deepARG using the github page but unsure what I would need to do within PathoFact to ge...Im having the same issue as issue #64 and the solution was to update deepARG 1.0.2 in bitbucket. I am using Ubuntu to run PathoFact. I tried updating deepARG using the github page but unsure what I would need to do within PathoFact to get it updated. I updated it and moved the files into the PathoFact folder where deepARG files are but this did not fix the problem. I've been able to run the toxin and virulence reports successfully. Appreciate any help!
"/mnt/d/Metagenomics_trial/PathoFact/.snakemake/conda/e658ef70/bin/deeparg", line 5, in from deeparg.entry import main File "/mnt/d/Metagenomics_trial/PathoFact/.snakemake/conda/e658ef70/lib/python2.7/site-packages/deeparg/entry.py", line 10, in import deeparg.predict.bin.deepARG as clf File "/mnt/d/Metagenomics_trial/PathoFact/.snakemake/conda/e658ef70/lib/python2.7/site-packages/deeparg/predict/bin/deepARG.py", line 21, in from deeparg.predict.bin import process_blast File "/mnt/d/Metagenomics_trial/PathoFact/.snakemake/conda/e658ef70/lib/python2.7/site-packages/deeparg/predict/bin/deeparg.py", line 21, in from deeparg.predict.bin import process_blast ImportError: No module named predict.binhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/92How to run PathoFact on Fasta file2022-09-19T15:07:54+02:00harelarikHow to run PathoFact on Fasta fileHi,
I have a fasta file of few proteins or DNA sequences, I have removed spaces from fasta headers.
PathoFact is installed in my linux system (version- Ubuntu 18.04).
conda version: 4.8.4 snakemake version 5.5.4
**How do I run Pathofact...Hi,
I have a fasta file of few proteins or DNA sequences, I have removed spaces from fasta headers.
PathoFact is installed in my linux system (version- Ubuntu 18.04).
conda version: 4.8.4 snakemake version 5.5.4
**How do I run Pathofact to scan the fasta file ?**
Thank you,
Arikhttps://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/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/90Error in rule R_script:2022-07-27T15:18:12+02:00fconstanciasError in rule R_script:Dear PathoFact developers,
Thanks for your effort developping that very usefull tool.
I am trying to use PathoFact using already annotated contigs i.e., ORFs `https://gitlab.lcsb.uni.lu/laura.denies/PathoFact/-/tree/orf`.
I prepared t...Dear PathoFact developers,
Thanks for your effort developping that very usefull tool.
I am trying to use PathoFact using already annotated contigs i.e., ORFs `https://gitlab.lcsb.uni.lu/laura.denies/PathoFact/-/tree/orf`.
I prepared the necessary files of a toy dataset: 1 sample of 1 contig and 2 orfs:
- [sample_megahit_253073.fna](/uploads/e6c28d4ad491c22879dc68453df60332/sample_megahit_253073.fna)
- [sample_megahit_253073.faa](/uploads/fc9948247ad375feffb374af7e3022b2/sample_megahit_253073.faa)
- [sample_megahit_253073.contig](/uploads/bae2f46278492afa8586d2bdd4f89ef4/sample_megahit_253073.contig)
and I am using the enclosed [config.yaml](/uploads/ef8a638779601905e8cb564986377a89/config.yaml)
I run the pipeline using ` snakemake -s Snakefile --use-conda --reason --cores 2 --configfile test_orfs_human1_1cont/config.yaml `
everything went smooth until the following error - [gene_table_library.log](/uploads/feee8f7c551d1112f4c5d581217119cd/gene_table_library.log) [2022-06-16T202537.905206.snakemake.log](/uploads/ce6e2a539b1f8691dfeab0e784a43c81/2022-06-16T202537.905206.snakemake.log)
```
[Thu Jun 16 20:26:42 2022]
Error in rule R_script:
jobid: 2
output: /datadrive05/Flo/tools/PathoFact_orf/test_orfs_human1_1cont/PathoFact_results_orf/PathoFact_report/Toxin_gene_library_sample_megahit_253073_report.tsv, /datadrive05/Flo/tools/PathoFact_orf/test_orfs_human1_1cont/PathoFact_results_orf/PathoFact_report/Toxin_prediction_sample_megahit_253073_report.tsv
log: /datadrive05/Flo/tools/PathoFact_orf/test_orfs_human1_1cont/PathoFact_results_orf/logs/sample_megahit_253073/gene_table_library.log (check log file(s) for error message)
conda-env: /datadrive05/Flo/tools/PathoFact_orf/.snakemake/conda/5f694c2e
RuleException:
CalledProcessError in line 29 of /datadrive05/Flo/tools/PathoFact_orf/rules/Toxin/Combine_Toxin_SignalP.smk:
Command 'source /home/constancias/miniconda3/envs/atlas-metagenomes/bin/activate '/datadrive05/Flo/tools/PathoFact_orf/.snakemake/conda/5f694c2e'; set -euo pipefail; Rscript --vanilla /datadrive05/Flo/tools/PathoFact_orf/.snakemake/scripts/tmp_ujrww4f.ownHMM_library.R' returned non-zero exit status 1.
File "/datadrive05/Flo/tools/PathoFact_orf/rules/Toxin/Combine_Toxin_SignalP.smk", line 29, in __rule_R_script
File "/home/constancias/miniconda3/envs/atlas-metagenomes/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:
/datadrive05/Flo/tools/PathoFact_orf/test_orfs_human1_1cont/PathoFact_results_orf/PathoFact_report/Toxin_gene_library_sample_megahit_253073_report.tsv
Activating conda environment: /datadrive05/Flo/tools/PathoFact_orf/.snakemake/conda/5f694c2e
```
Thanks for your help.
EDIT: My test dataset works well using `AMR` and `VIR` workflows.
EDIT2: Might be worth to add an orf test dataset for the `https://gitlab.lcsb.uni.lu/laura.denies/PathoFact/-/tree/orf` branch.