PathoFact issueshttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues2021-04-12T14:22:45+02:00https://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/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/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/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/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/38size_fasta is not used by seqkit2020-06-11T15:40:51+02:00Valentina Galatavalentina.galata@uni.lusize_fasta is not used by seqkitThe parameter `size_fasta` from the config file is not used in any of the rules.
All `seqkit split2` calls contain `-s 10000`The parameter `size_fasta` from the config file is not used in any of the rules.
All `seqkit split2` calls contain `-s 10000`Paper review - Microbiome - 1Valentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/31spring-clean: args in virulence_prediction.py and rule classifier in the vir ...2020-04-23T12:32:59+02:00Valentina Galatavalentina.galata@uni.luspring-clean: args in virulence_prediction.py and rule classifier in the vir stepScript `scripts/virulence_prediction.py` uses `snakemake` variable to access parameters but the rule `classfier` in `rules/Virulence/Virulence.snk` uses `shell` instead of `script`.Script `scripts/virulence_prediction.py` uses `snakemake` variable to access parameters but the rule `classfier` in `rules/Virulence/Virulence.snk` uses `shell` instead of `script`.spring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.lu