violin plot fail

[terooatt]

[terooatt]

Hi,

I somehow can't seem able to run the violin plot properly. Here is the error I get.

snakemake --cores 8 --use-conda --directory ~/Nadia_analysis/dropSeqPipe ..... ..... Activating conda environment:/home/Nadia_analysis/dropSeqPipe/.snakemake/conda/c4d744c4

Attaching package: ‘cowplot’

The following object is masked from ‘package:ggplot2’:

ggsave

Error in grDevices::pdf(..., version = version) : cannot open file '/home/Nadia_analysis/dropSeqPipe//home/Nadia_analysis/4_nuclei_heart_hiseq/results/plots/UMI_vs_counts.pdf' Calls: ggsave -> do.call -> <Anonymous> -> dev -> <Anonymous> Execution halted [Thu Jun 20 17:05:58 2019] Error in rule violine_plots: jobid: 15 output: /home/Nadia_analysis/4_nuclei_heart_hiseq/results/plots/violinplots_comparison_UMI.pdf, /home/Nadia_analysis/4_nuclei_heart_hiseq/results/plots/UMI_vs_counts.pdf, /home/Nadia_analysis/4_nuclei_heart_hiseq/results/plots/UMI_vs_gene.pdf, /home/Nadia_analysis/4_nuclei_heart_hiseq/results/plots/Count_vs_gene.pdf, /home/Nadia_analysis/4_nuclei_heart_hiseq/results/summary/R_Seurat_objects.rdata conda-env: /home/Nadia_analysis/dropSeqPipe/.snakemake/conda/c4d744c4

Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /home/Nadia_analysis/dropSeqPipe/.snakemake/log/2019-06-20T170543.011943.snakemake.log

[Hoohm]

Hello @terooatt this is an often problem encountered with different platforms, I had the same issue on my cluster server.

Could you please tell us which OS is running on the computer you are using?

[seb-mueller]

This seems to be the same as issue #71. @Hoohm, Could you have a look at this issue? This has been fixed but the branch (which is only at my fork) seems not merged in yet. Not sure why we didn't do this, I could do a pull request if you agree (Or did I miss something?). The branch is (https://github.com/seb-mueller/dropSeqPipe/tree/feature/newline_plus_yield_bugfix) and the relevant commit solving this issue is https://github.com/seb-mueller/dropSeqPipe/commit/7a537ec83aeee045631fa7608ffb157cf932bcfd

@terooatt , could you pull the above mentioned branch and see if the fixes the problem?

[abmmki]

Hi I am using fedora 30. I got different type of error:

Registered S3 method overwritten by 'R.oo': method from
throw.default R.methodsS3 Error in CreateSeuratObject(raw.data = umi_matrix, meta.data = metaData) : unused argument (raw.data = umi_matrix) Execution halted [Sat Jul 27 03:23:04 2019] Error in rule violine_plots: jobid: 55

[seb-mueller]

Just had another look and commit 7a537ec has in fact been merged, so #71 is not the culprit anymore. But as of the last message of @abmmki , it's the same error now as in #84.

[Hoohm]

Is this fixed? Can I close it?

[TomKellyGenetics]

@terooatt and I are in the same lab, we're running the pipeline on the same Debian server. I think this was the same issue I had so it is safe to close.