Skip to content

GitLab

I
IMP
Closed
Opened by Shaman Narayanasamy@shaman.narayanasamy
Report abuse New issue

NoFiltering rule issue

The Nofiltering rule doesn't seem to be working. I get the following error:

rule PREPROCESSING_NO_FILTER:
	input: /output/Preprocessing/MG.R1.trimmed.fq, /output/Preprocessing/MG.R2.trimmed.fq, /output/Preprocessing/MG.SE.trimmed.fq, /output/Preprocessing/MT.R1.trimmed.rna_filtered.fq, /output/Preprocessing/MT.R2.trimmed.rna_filtered.fq, /output/Preprocessing/MT.SE.trimmed.rna_filtered.fq
	output: /output/Preprocessing/MG.R1.preprocessed.fq, /output/Preprocessing/MG.R2.preprocessed.fq, /output/Preprocessing/MG.SE.preprocessed.fq, /output/Preprocessing/MT.R1.preprocessed.fq, /output/Preprocessing/MT.R2.preprocessed.fq, /output/Preprocessing/MT.SE.preprocessed.fq
	log: /output/Preprocessing/Preprocessing.log
	benchmark: /output/Preprocessing/benchmarks/PREPROCESSING_NO_FILTER.json
8 of 43 steps (19%) done
Traceback (most recent call last):
  File "/usr/local/lib/python3.4/dist-packages/snakemake/__init__.py", line 379, in snakemake
    greediness=greediness)
  File "/usr/local/lib/python3.4/dist-packages/snakemake/workflow.py", line 427, in execute
    success = scheduler.schedule()
  File "/usr/local/lib/python3.4/dist-packages/snakemake/scheduler.py", line 203, in schedule
    run = self.job_selector(needrun)
  File "/usr/local/lib/python3.4/dist-packages/snakemake/scheduler.py", line 322, in job_selector
    c = list(map(self.job_reward, jobs))  # job rewards
  File "/usr/local/lib/python3.4/dist-packages/snakemake/scheduler.py", line 404, in job_reward
    job.inputsize)
  File "/usr/local/lib/python3.4/dist-packages/snakemake/jobs.py", line 93, in inputsize
    self._inputsize = sum(map(os.path.getsize, self.input))
  File "/usr/lib/python3.4/genericpath.py", line 50, in getsize
    return os.stat(filename).st_size
FileNotFoundError: [Errno 2] No such file or directory: '/output/Preprocessing/MT.R1.trimmed.rna_filtered.fq'

The strange thing is that the files actually exist...

This is confusing. When I run the steps indivudually, there seems to be no issue. But, when I simply launch snakemake, i.e. all the steps, it crashes because it runs almost all the preprocessing steps all over again. I guess this is because snakemake is looking for those intermediate preprocessed fastq files, but does not find it :(

Linked issues