PathoFact issueshttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues2023-05-28T23:22:25+02:00https://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/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/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/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/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/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.https://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/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/86qsub: Bad UID for job execution2022-03-02T08:31:14+01:00Gaoyang Luoqsub: Bad UID for job executionDear @laura.denies
I wanted to put it on the cluster with cmd:qsub but failed.
"Error submitting jobscript (exit code 175)"
Here is my .pbs file[pathofact.pbs](/uploads/3d01605374f6c2b95f8f7def569573a5/pathofact.pbs)
And here is the err...Dear @laura.denies
I wanted to put it on the cluster with cmd:qsub but failed.
"Error submitting jobscript (exit code 175)"
Here is my .pbs file[pathofact.pbs](/uploads/3d01605374f6c2b95f8f7def569573a5/pathofact.pbs)
And here is the error log[pathofact_AMR.e284271](/uploads/7c4a3d02ff19b7ae2e9fab191a1075a3/pathofact_AMR.e284271)https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/85Error in rule splitting2022-03-02T08:31:24+01:00Gaoyang LuoError in rule splittingError in rule splitting:
jobid: 30
output: path/PathoFact_results/splitted/SRR3401469.contigs/
log: path/test/PathoFact_results/logs/SRR3401469.contigs/split_ORF.log (check log file(s) for error message)
conda-env: path/Patho...Error in rule splitting:
jobid: 30
output: path/PathoFact_results/splitted/SRR3401469.contigs/
log: path/test/PathoFact_results/logs/SRR3401469.contigs/split_ORF.log (check log file(s) for error message)
conda-env: path/PathoFact/.snakemake/conda/a010a931
shell:
python scripts/split.py path/PathoFact_results/PathoFact_intermediate/renamed/SRR3401469.contigs_ID.faa 10000 path/PathoFact_results/splitted/SRR3401469.contigs/ &> path/PathoFact_results/logs/SRR3401469.contigs/split_ORF.log
(exited with non-zero exit code)
Updating job 18.
Updating job 19.
Creating conda environment envs/HMMER.yaml...
Downloading remote packages.
[Thu Feb 24 19:39:58 2022]
Error in rule splitting:
jobid: 28
output: path/PathoFact_results/PathoFact_intermediate/splitted/SRR3401469.contigs/
log: path/PathoFact_results/PathoFact_intermediate/logs/SRR3401469.contigs/split_ORF.log (check log file(s) for error message)
conda-env: path/PathoFact/.snakemake/conda/a010a931
shell:
python scripts/split.py path/PathoFact_results/PathoFact_intermediate/PathoFact_intermediate/renamed/SRR3401469.contigs_ID.faa 10000 path/PathoFact_results/PathoFact_intermediate/splitted/SRR3401469.contigs/ &> path/PathoFact_results/PathoFact_intermediate/logs/SRR3401469.contigs/split_ORF.log
(exited with non-zero exit code)
Removing output files of failed job splitting since they might be corrupted:
path/PathoFact_results/splitted/SRR3401469.contigs/
Removing output files of failed job splitting since they might be corrupted:
path/PathoFact_results/PathoFact_intermediate/splitted/SRR3401469.contigs/
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /lomi_home/gaoyang/software/PathoFact/.snakemake/log/2022-02-24T184853.821696.snakemake.loghttps://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/73only small fasta files (around 6000~7000 contigs) can work in Vir and Tox module2021-08-31T15:59:32+02:00Xuanji Lionly small fasta files (around 6000~7000 contigs) can work in Vir and Tox moduleDear Developer
The test file you offered in PathoFact can work. but when I run my own input metagenomic sample (with 2.5M contigs), it always gives me errors. So I tried to split the sample into a couple of small files. I found only smal...Dear Developer
The test file you offered in PathoFact can work. but when I run my own input metagenomic sample (with 2.5M contigs), it always gives me errors. So I tried to split the sample into a couple of small files. I found only small files with < 6000-7000 contigs can work. The error seems to be from signalp (as below), but when I run my big contig sample by signal separately, it can work. So really weird. Do you have any ideas on how to solve this? because I have >600 metagenomics samples.
Thanks
![LS4XC95SSCWDNCXZ9A185ZK](/uploads/5f6b0a9b5b4dfefe38079da8c031d827/LS4XC95SSCWDNCXZ9A185ZK.png)https://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/70Unclassified MGE2021-08-28T18:42:01+02:00ntromasUnclassified MGEHi,
Is it possible to know a bit more of how are classified MGEs. I saw the cutoff for PlasFlow but what about the one for phage? I have increased the PlasFlow cutoff to 0.9 as I have env metagenomic data but I have now a huge proportio...Hi,
Is it possible to know a bit more of how are classified MGEs. I saw the cutoff for PlasFlow but what about the one for phage? I have increased the PlasFlow cutoff to 0.9 as I have env metagenomic data but I have now a huge proportion of unclassified. When you tested PathoFact, did you also observe a large proportion of unclassified?
Thanks for your help,
Nicohttps://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/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/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/64testing module fails with DeepARG2022-04-15T23:44:16+02:00mhmismtesting module fails with DeepARGHello,
Thank you for this nice tool.
I have run the testing modules, but it fails at the DeepARG step, and it fails completely afterward.
Here is the logfile associated with DeepARG (group_1.out.mapping.ARG):
/mnt/d/Metagenomics_tr...Hello,
Thank you for this nice tool.
I have run the testing modules, but it fails at the DeepARG step, and it fails completely afterward.
Here is the logfile associated with DeepARG (group_1.out.mapping.ARG):
/mnt/d/Metagenomics_trial/PathoFact/.snakemake/conda/e658ef70/lib/python2.7/site-packages/theano/tensor/signal/downsample.py:6: UserWarning: downsample module has been moved to the theano.tensor.signal.pool module.
"downsample module has been moved to the theano.tensor.signal.pool module.")
/mnt/d/Metagenomics_trial/PathoFact/.snakemake/conda/e658ef70/lib/python2.7/site-packages/sklearn/cross_validation.py:41: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. Also note that the interface of the new CV iterators are different from that of this module. This module will be removed in 0.20.
"This module will be removed in 0.20.", DeprecationWarning)
Traceback (most recent call last):
File "/mnt/d/Metagenomics_trial/PathoFact/.snakemake/conda/e658ef70/bin/deeparg", line 5, in <module>
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 <module>
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 <module>
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 <module>
from deeparg.predict.bin import process_blast
ImportError: No module named predict.binhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/63How estimate relative abundance?2021-09-10T18:51:28+02:00AA8898How estimate relative abundance?Hello everyone,
I do not really understand how it is possible to estimate the relative abundance of virulence factore, bacterial toxins and AMR?
Is it a way within the PathoFact pipeline to calculate it or do I have to use another pipeli...Hello everyone,
I do not really understand how it is possible to estimate the relative abundance of virulence factore, bacterial toxins and AMR?
Is it a way within the PathoFact pipeline to calculate it or do I have to use another pipeline for that?
thanks a lothttps://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.lu