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nanoporetech / pipeline-transcriptome-de

Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
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The pipeline was abruptly terminated in the first step #7

Closed weir12 closed 5 years ago

weir12 commented 5 years ago

Hi When I run snakemake, the program terminates after completing the first step, but no errors are raised.

Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 8
Rules claiming more threads will be scaled down.
Job counts:
        count   jobs
        1       dump_versions
        1

[Sat Jun  8 20:58:14 2019]
rule dump_versions:
    output: versions.txt
    jobid: 0

[Sat Jun  8 20:58:29 2019]
Finished job 0.
1 of 1 steps (100%) done

Then I try to manually run the second step (snakemake -j 8 -f build_minimap_index ), the minimap index is correctly established without error.

weir12 commented 5 years ago

Hi I have figured out the cause of the problem and solved it. The following rule should be executed as the first rule before all other rules.This solution is at least effective for me. https://github.com/nanoporetech/pipeline-transcriptome-de/blob/fc6d6c4f1d005cd3c406ee1912314e468a4b60e6/Snakefile#L151-L159