Error on rule fastq: outputs of incorrect type

[Former user]

Hi,

I downloaded the configured workflow and encountered the following error (which I also had when using my own data: ImproperOutputException in line 31 of /mageck-vispr/esc-testdata/Snakefile: Outputs of incorrect type (directories when expecting files or vice versa). Output directories must be flagged with directory(). for rule fastqc: results/qc/esc1_0 Removing output files of failed job fastqc since they might be corrupted: results/qc/esc1_0 [Errno 66] Directory not empty: 'results/qc/esc1_0'

The log file ends as follows:

INFO @ Mon, 14 Jan 2019 20:34:51: Loading Rnw template file: /Users/kbalbosa/miniconda3/envs/mageck-vispr/lib/python3.6/site-packages/mageck/fastq_template.Rnw.

I am using conda 4.5.12 and updated mageck-vispr prior to running.

Thank you for your support,

Karina Barbosa

[Former user]

Hi, I'm having the same issue as Karina.

[Rishabh Gupta]

Facing the same issue.

To get past this, I just run the command “snakemake --cores num_of_threads” again and it starts working fine

Environment:

Conda: 4.6.14

Mageck-VISPR: 0.5.4

[Catherine]

I uninstalled snakemake version 5.2 and installed version 5.1.5 and it seems to work now, but there’s no mageck_count job in it now, not sure if I screwed up or what.

pip3 uninstall snakemake
pip3 install -Iv snakemake==5.1.5

[Johnny Tkach]

Same issue here. Re-running snakemake does not help. Also commented on issue #57 - same as this one.

Any help appreciated,

Johnny