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dib-lab / elvers

(formerly eelpond) an automated RNA-Seq workflow system
https://dib-lab.github.io/elvers/
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Missing input files for rule deseq2_init_tx2gene #90

Closed johnsolk closed 5 years ago

johnsolk commented 5 years ago 
(eelpond-sw) diblions@js-169-30:~/eelpond$ ./run_eelpond quant_DE.yml diffexp

--------
checking for required files:
--------

        Found input assembly at ../data/nema_trinity.fasta
        Added default parameters from rule-specific params files.
        Writing full params to .ep_quant_DE.yml
--------
details!
        snakefile: /home/diblions/eelpond/Snakefile
        config: quant_DE.yml
        params: .ep_quant_DE.yml
        targets: ['diffexp', 'assemblyinput']
        report: '/home/diblions/eelpond/lab7_out_quant_DE/logs/report.html'
--------
/opt/miniconda/envs/eelpond-sw/lib/python3.6/site-packages/snakemake/workflow.py:23: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'.
  from snakemake.shell import shell
Building DAG of jobs...
MissingInputException in line 34 of /home/diblions/eelpond/rules/deseq2/deseq2.rule:
Missing input files for rule deseq2_init_tx2gene:
/home/diblions/eelpond/lab7_out_quant_DE/assembly/lab7_input.fasta.gene_trans_map
bluegenes commented 5 years ago

Hi @ljcohen, can you paste in the quant_DE.yml file for this please? We need to either provide the gene_trans_map or set the deseq2 gene_trans_map parameter to false. https://dib-lab.github.io/eelpond/diffexp, https://dib-lab.github.io/eelpond/deseq2

johnsolk commented 5 years ago

Setting gene_trans_map=false solved this problem. Here is the .yml created with ./run_eelpond quant_DE.yml quantify (which then crashed because of #89)

  ####################  Eelpond Pipeline Configfile  ####################  
basename: lab7
experiment: DE
samples: samples.tsv

  ####################  diffexp  ####################  
deseq2:
  contrasts:
    time0-vs-time6:
    - time0
    - time6
  gene_trans_map: false
  pca:
    labels:
    - condition
get_data:
  download_data: false
  use_ftp: false
salmon:
  index_params:
    extra: ''
  input_trimmomatic_trimmed: true
  quant_params:
    extra: ''
    libtype: A
trimmomatic:
  adapter_file:
    pe_path: ep_utils/TruSeq3-PE-2.fa
    se_path: ep_utils/TruSeq3-SE.fa
  extra: ''
  trim_cmd: ILLUMINACLIP:{}:2:40:15 LEADING:2 TRAILING:2 SLIDINGWINDOW:4:15 MINLEN:25
assemblyinput:
  assembly: '../data/nema_trinity.fasta'
  assembly_extension: '_input'
bluegenes commented 5 years ago

fyi @ljcohen, the alternative would be to have this in the yaml:

assemblyinput:
  assembly: '../data/nema_trinity.fasta'
  gene_trans_map: '../data/nema_trinity.fasta.gene_trans_map'
  assembly_extension: '_input'

eelpond just needs to know where to find the gene_trans_map, if using it