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liulab-dfci / CHIPS

A Snakemake pipeline for quality control and reproducible processing of chromatin profiling data
MIT License
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InputFunctionException in line 242 of .../CHIPS/chips.snakefile #1

Closed mdozmorov closed 3 years ago

mdozmorov commented 3 years ago

Hi. I'm trying CHIPS on single-end ATAC-seq data, and got the following error:

(chips) -bash-4.1$ snakemake -np  -s CHIPS/chips.snakefile --rerun-incomplete
fastp 0.20.1
/home/../miniconda3/envs/chips/lib/python3.6/site-packages/snakemake/workflow.py:743: DtypeWarning: Columns (1,2,7) have mixed types.Specify dtype option on import or set low_memory=False.
  exec(compile(code, snakefile, "exec"), self.globals)
Gapdh found in bed
Actb found in bed
Trp53 found in bed
Homer module is being used and details file was copied.
Homer module is being run.
Building DAG of jobs...
InputFunctionException in line 242 of /home/sequencing/ATAC_seq/CHIPS/chips.snakefile:
KeyError: 'S1_S1_R1_001.fastq.gz'
Wildcards:

I'm rather new to Snakemake, so not sure what to do about it. The filenames look correct in config.yaml., and it is not the first file the error is thrown.

Thanks, Mikhail

mdozmorov commented 3 years ago

A couple of previous errors that I was able to fix.

(chips) -bash-4.1$ snakemake -np  -s CHIPS/chips.snakefile --rerun-incomplete
FileNotFoundError in line 72 of /home/sequencing/ATAC_seq/CHIPS/chips.snakefile:
[Errno 2] No such file or directory: 'cidc_chips/ref.yaml'

This is caused by line 3 in config.yaml. The hard-coded cidc_chips should be removed, because the ref.yaml is in the project directory.

The other error was similar:

(chips) -bash-4.1$ snakemake -np  -s CHIPS/chips.snakefile --rerun-incomplete
fastp 0.20.1
FileNotFoundError in line 81 of /home/sequencing/ATAC_seq/CHIPS/modules/new_report.snakefile:
[Errno 2] No such file or directory: 'cidc_chips/report/ref_assembly.csv'

So, I changed cidc_chips to CHIPS. Then, the reported error occurred.

liulab-dfci commented 3 years ago

Hi Mikhail, can you please try the most recent version in this repo? I moved the repo from bitbucket to github and there are some bugs need to be fixed (e.g, cidc_chips). ---Tommy

crazyhottommy commented 3 years ago

Hi Mikhail, now the paper is on F1000 https://f1000research.com/articles/10-517/v1 there are examples there, may be helpful for you.

mdozmorov commented 3 years ago

Congratulations, Ming, for publishing it, and thank you for sharing! I trust this issue is fixed, will close. CHIPS is still on my list, waiting for new data. Closer to the top is MAESTRO, we are getting some scRNA and scATAC-seq.

crazyhottommy commented 3 years ago

Thanks! sounds good. let us know anything we can help with!