ImproperOutputException error when running snakemake --cores 8

[Former user]

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.

[Johnny Tkach]

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

[Johnny Tkach]

Hi all. Seemed to fix the error, however I’m not quite what actually fixed the problem. Here is what I did…

1. Remove MAGeCK-vispr environment

   1. conda remove -n mageck-vispr -all

2. change channel order in bioconda *** note that there are different instructions for this in different places *** (bioconda page compared to Nature Protocols paper)

   1. conda config --add channels default
   2. conda config --add channels conda-forge
   3. conda config --add channels bioconda

3. Create MAGeCK-vispr environment

   1. conda create -n mageck-vispr mageck-vispr

4. activate environment

   1. conda activate mageck-vispr

5. update everything

   1. conda update mageck-vispr
   2. 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.

[Alex Brown]

I also had this problem but Johnny’s fix seems to have worked. Many thanks!

[matthew McTaggart]

+ 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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[cmonger]

+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