ImproperOutputException error when running snakemake --cores 8
Even though apparently my config.yaml file has been edited correctly (I get no error when running snakemake -n), I get the following error when executing the workflow (snakemake --cores 8) for every sample:
ImproperOutputException in line 31 of /home/jjp12/Documents/MIRABAI/CRISPR_KO_screen/workflow/Snakefile: Outputs of incorrect type (directories when expecting files or vice versa). Output directories must be flagged with directory(). for rule fastqc: results/qc/LOW2_0 Removing output files of failed job fastqc since they might be corrupted: results/qc/LOW2_0 Skipped removing non-empty directory results/qc/LOW2_0
My version of mageck-vispr is 0.5.3.
Thanks in advance.
Comments (5)
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Hi all. Seemed to fix the error, however I’m not quite what actually fixed the problem. Here is what I did…
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Remove MAGeCK-vispr environment
- conda remove -n mageck-vispr -all
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change channel order in bioconda *** note that there are different instructions for this in different places *** (bioconda page compared to Nature Protocols paper)
- conda config --add channels default
- conda config --add channels conda-forge
- conda config --add channels bioconda
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Create MAGeCK-vispr environment
- conda create -n mageck-vispr mageck-vispr
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activate environment
- conda activate mageck-vispr
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update everything
- conda update mageck-vispr
- conda update mageck
After doing this, the analysis worked for me, but the visualization step gave me an error. To fix this, install older version of pandas:
pip install pandas==0.19.2
Best of luck. I hope this works for you.
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I also had this problem but Johnny’s fix seems to have worked. Many thanks!
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+ 1 to the fix working
I read some other forums with the same problem. It seems the snakemake version might have something to do with it. Following the original instructions snakmake --version returned 5.xx however following the fix by @Johnny Tkach returns 4.0.0
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+1
Had to use mamba to install however due to the solving dependancy issue:
mamba create -n mageck-vispr mageck-vispr
Seems to be working now. Thanks Johnny
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Same error here. Of the 6 fastq samples I’m analyzing, three have FastQC folders (they happen to be the ‘controls’). The reads are mapped, counted and normalized, but no further analysis occurs.
Mageck-vispr is up to date and running on Mac OSX.
Thanks,
Johnny