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Hoohm / dropSeqPipe

A SingleCell RNASeq pre-processing snakemake workflow
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Another type of violin plot failure #89

Open Hofphi opened 5 years ago

Hofphi commented 5 years ago

Hello everyone,

I have encountered a violin plot failure which I am unable to resolve. I was able to generate the plot with previous data but suddenly the pipeline gives an error at this process and shuts down.

This is the error message:

Error in rule violine_plots:
    jobid: 13
    output: /mnt/DATA/DropSeq_Philipp/dropSeqPipe_v04/results/plot/violinplots_comparison_UMI.pdf,
            /mnt/DATA/DropSeq_Philipp/dropSeqPipe_v04/results/plots/UMI_vs_counts.pdf,
            /mnt/DATA/DropSeq_Philipp/dropSeqPipe_v04/results/plots/UMI_vs_gene.pdf, 
            /mnt/DATA/DropSeq_Philipp/dropSeqPipe_v04/results/plots/Count_vs_gene.pdf,
            /mnt/DATA/DropSeq_Philipp/dropSeqPipe_v04/results/summary/R_Seurat_objects.rdata
    conda-env: /mnt/DATA/DropSeq_Philipp/dropSeqPipe_v04/.snakemake/conda/188c153d

RuleException:
CalledProcessError in line 32 of /mnt/DATA/DropSeq_Philipp/dropSeqPipe_v04/rules/merge.smk:
Command 'source activate /mnt/DATA/DropSeq_Philipp/dropSeqPipe_v04/.snakemake/conda/188c153d; set -euo pipefail; 
         Rscript --vanilla /mnt/DATA/DropSeq_Philipp/dropSeqPipe_v04/.snakemake/scripts/tmp7u_of87x.plot_violine.R ' 
  returned non-zero exit status 1.
  File "/mnt/DATA/DropSeq_Philipp/dropSeqPipe_v04/rules/merge.smk", line 32, in __rule_violine_plots
  File "/home/kirstin/Tools/anaconda3/lib/python3.6/concurrent/futures/thread.py", line 56, in run

I already tried to manually execute the R-script:

source activate /mnt/DATA/DropSeq_Philipp/dropSeqPipe_v04/.snakemake/conda/188c153d
Rscript --vanilla /mnt/DATA/DropSeq_Philipp/dropSeqPipe_v04/.snakemake/scripts/tmp7u_of87x.plot_violine.R

Which gives me that error:

/mnt/DATA/DropSeq_Philipp/dropSeqPipe_v04/.snakemake/scripts/tmp7u_of87x.plot_violine.R': No such file or directory

The summary folder contains the needed files, that's why I don't get the error message. I am running DropSeqPipe_v0.4.

I would appreciate your help.

Hofphi commented 5 years ago

I am seem to miss this file:

/mnt/DATA/DropSeq_Philipp/dropSeqPipe_v04/.snakemake/scripts/tmpahs41u48.plot_violine.R

Shouldn't this temporary script be generated as soon as I start the pipeline. All files needed to make the plot do exist in the results/summary directory.

Hoohm commented 5 years ago

Hello @Hofphi you have nto changed anything and you get a new error?

You can't try and run the temporary R script file because it's getting deleted by snakemake on the fly.

There is a new debug feature coming up in the new release but is already implementd on the develop branch if you want to try it out.

It helps with those kinds of issues by creating an rdata file of the snakemake object before the script as well as one when it's done running.

You can then easily load up the rdata file into R or Rstudio and run the script line by line to check what's wrong.

The error message you shared here is only snakemake telling us that something went wrong, but we would need to investigate what the error is the R script.