Error with a particular short read assembly.gfa file
Hello,
I was able to successfully install gPlas and it worked very well for me to analyze Illumina reads that had been assembled using SPAdes.
However, one particular assembly provided me with the following error:
Error in rule gplas_coocurr: jobid: 0 output: results/EC25_illumina_gplas_plasmidome_network.png, results/EC25_illumina_gplas_bins.tab, results/EC25_illumina_gplas_results.tab conda-env: /home/kringwa2/gplas/.snakemake/conda/08b79d10
RuleException: CalledProcessError in line 126 of /home/kringwa2/gplas/mlplasmidssnake.smk: Command 'source /home/kringwa2/miniconda3/bin/activate '/home/kringwa2/gplas/.snakemake/conda/08b79d10'; set -euo pipefail; Rscript --vanilla /home/kringwa2/gplas/.snakemake/scripts/tmpcx_s1e5o.gplas_coocurrence.R' returned non-zero exit status 1. File "/home/kringwa2/gplas/mlplasmidssnake.smk", line 126, in __rule_gplas_coocurr File "/home/kringwa2/miniconda3/envs/gplas/lib/python3.7/concurrent/futures/thread.py", line 57, in run Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /home/kringwa2/gplas/.snakemake/log/2020-09-30T163004.213360.snakemake.log "
I have pasted the contents of the resulting snakemake log file:
" The flag 'directory' used in rule awk_parsing_alignment is only valid for outputs, not inputs. Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 1 Rules claiming more threads will be scaled down. Job counts: count jobs 1 gplas_coocurr 1
[Wed Sep 30 16:30:04 2020] Job 0: Generating weights for the set of new edges connecting plasmid unitigs
Activating conda environment: /home/kringwa2/gplas/.snakemake/conda/08b79d10 [Wed Sep 30 16:30:16 2020] Error in rule gplas_coocurr: jobid: 0 output: results/EC25_illumina_gplas_plasmidome_network.png, results/EC25_illumina_gplas_bins.tab, results/EC25_illumina_gplas_results.tab conda-env: /home/kringwa2/gplas/.snakemake/conda/08b79d10
RuleException: CalledProcessError in line 126 of /home/kringwa2/gplas/mlplasmidssnake.smk: Command 'source /home/kringwa2/miniconda3/bin/activate '/home/kringwa2/gplas/.snakemake/conda/08b79d10'; set -euo pipefail; Rscript --vanilla /home/kringwa2/gplas/.snakemake/scripts/tmpcx_s1e5o.gplas_coocurrence.R' returned non-zero exit status 1. File "/home/kringwa2/gplas/mlplasmidssnake.smk", line 126, in __rule_gplas_coocurr File "/home/kringwa2/miniconda3/envs/gplas/lib/python3.7/concurrent/futures/thread.py", line 57, in run Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /home/kringwa2/gplas/.snakemake/log/2020-09-30T163004.213360.snakemake.log "
Thanks for your time and the excellent tool. Ken R