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Created by Matthew Macowan@mmac0026

hmm.R

Hi, I just got this error, and I'm wondering if it is similar to previously closed issues #62 (closed) and #39 (closed).

Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 16
Rules claiming more threads will be scaled down.
Job counts:
	count   jobs
        1	HMM_R_VIR
        1
[Sat Jul 31 01:59:24 2021]
rule HMM_R_VIR:
    input: /fs03/mf33/Matt/sunbeam_cf_shotgun/sunbeam_output/assembly/contigs/PathoFact_results/PathoFact_intermediate/VIRULENCE/HMM_virulence/181s4_S72-co$
    output: /fs03/mf33/Matt/sunbeam_cf_shotgun/sunbeam_output/assembly/contigs/PathoFact_results/PathoFact_intermediate/VIRULENCE/HMM_virulence/181s4_S72-c$
    log: /fs03/mf33/Matt/sunbeam_cf_shotgun/sunbeam_output/assembly/contigs/PathoFact_results/logs/181s4_S72-contigs/hmm_results.log
    jobid: 0
    wildcards: project=PathoFact_results, sample=181s4_S72-contigs
Rscript --vanilla /fs03/mf33/Matt/PathoFact/.snakemake/scripts/tmp02b99mr2.hmm.R
Activating conda environment: /fs03/mf33/Matt/PathoFact/.snakemake/conda/7950189c
/fs03/mf33/Matt/PathoFact/.snakemake/conda/7950189c/lib/R/bin/R: line 240: /fs03/mf33/Matt/PathoFact/.snakemake/conda/7950189c/lib/R/etc/ldpaths: No such f$
[Sat Jul 31 01:59:50 2021]
Error in rule HMM_R_VIR:
    jobid: 0
    output: /fs03/mf33/Matt/sunbeam_cf_shotgun/sunbeam_output/assembly/contigs/PathoFact_results/PathoFact_intermediate/VIRULENCE/HMM_virulence/181s4_S72-c$
    log: /fs03/mf33/Matt/sunbeam_cf_shotgun/sunbeam_output/assembly/contigs/PathoFact_results/logs/181s4_S72-contigs/hmm_results.log (check log file(s) for$
    conda-env: /fs03/mf33/Matt/PathoFact/.snakemake/conda/7950189c
RuleException:
CalledProcessError in line 87 of /fs03/mf33/Matt/PathoFact/rules/Virulence/Virulence.smk:
Command 'source /scratch/of33/mmacowan/miniconda/bin/activate '/fs03/mf33/Matt/PathoFact/.snakemake/conda/7950189c'; set -euo pipefail;  Rscript --vanilla $
  File "/fs03/mf33/Matt/PathoFact/rules/Virulence/Virulence.smk", line 87, in __rule_HMM_R_VIR
  File "/scratch/of33/mmacowan/miniconda/envs/PathoFact/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

It looks like line 87 refers to script hmm.R.

The hmm_results.log file for the particular instance that caused the error was present but empty, however this is the contents of that file for one of the other samples:

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()
Attaching package: 'reshape2'
The following object is masked from 'package:tidyr':
    smiths

Have you encountered a similar issue? Any help would be greatly appreciated.

Thanks, Matthew