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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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A question about setting of config.yml #2

Closed weir12 closed 5 years ago

weir12 commented 5 years ago

Hi Botond,

I was in a trouble when I tried to run sankefile like this: $ snakemake --use-conda -j 4 all Error Report:

 Building DAG of jobs...
 MissingInputException in line 23 of /home/weir/software/pipeline-transcriptome-de/Snakefile:
 Missing input files for rule build_minimap_index:
 Araport11_genes.201606.cdna.fasta

Attached my config.yml 

---
## General pipeline parameters:

# Name of the pipeline:
pipeline: "Nanopore-DES-Analysis"
# ABSOLUTE path to directory holding the working directory:
workdir_top: "/home/weir/output/"
# Results directory:
resdir: "/home/weir/output/Nanopore-DEG-Analysis/result_DEG"
# Repository URL:
repo: "https://github.com/nanoporetech/pipeline-transcriptome-de"

## Pipeline-specific parameters:

transcriptome: "Araport11_genes.201606.cdna.fasta"
annotation: "Araport11_GFF3_genes_transposons.gtf"

control_samples:
    Col0_1: "col0_1.fastq"
    Col0_2: "col0_2.fastq"
    Col0_3: "col0_3.fastq"

treated_samples:
    fip37_1: "fip37_1.fastq"
    fip37_2: "fip37_2.fastq"
    fip37_3: "fip37_3.fastq"

minimap_index_opts: ""

minimap2_opts: "-ax splice -uf -k14 ref.fa direct-rna.fq"

maximum_secondary: 100

secondary_score_ratio: 1.0

salmon_libtype: "SF"

# Count filtering options - customize these according to your experimental design:

# Genes expressed in minimum this many samples:
min_samps_gene_expr: 3
# Transcripts expressed in minimum this many samples:
min_samps_feature_expr: 1
# Minimum gene counts:
min_gene_expr: 10
# Minimum transcript counts:
min_feature_expr: 3

threads: 8

The transcripts and annotations were downloaded from:(https://www.arabidopsis.org/) minimap2 --version :2.15-r905 snakemake was installed by conda(4.6.7). All my input files are exist in /home/weir/output/Nanopore-DEG-Analysis/ In addition,I successfully tried manually indexing ref.fa by minimap2 command: minimap2 -d ref.mmi ref.fa

bsipos commented 5 years ago

Hi!

You have to specify the absolute path to the files, such as: transcriptome: "/home/weir/output/Nanopore-DEG-Analysis/Araport11_genes.201606.cdna.fasta"

Also, minimap2_opts should be only "-uf -k14" and minimap_index_opts should be "-k14".

Best, Botond

bsipos commented 5 years ago

Hello!

Pandas is a dependency which has to be present in the environment from which you are invoking snakemake. It is not necessary to install it in the environment created by --use-conda.

Botond