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fiberseq / fibertools-rs

Tools for fiberseq data written in rust.
https://fiberseq.github.io/fibertools/fibertools.html
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MissingInputException error when running fiberseq-smk #62

Closed AnnaE-F closed 2 months ago

AnnaE-F commented 2 months ago

Hello, I am trying to run snakemake (on linux, on a cluster) and I am facing a "MissingInputException" error. I have seen several similar issues reported on the internet but I don't know how to fix mine.

This is what I typed:

sbatch [options] \ snakemake --profile profile/compute \ --config env="fiberseq-smk" \ anna_sub_1=[path to my bam file] \ ref=[path to my reference]

and here is the error message:

MissingInputException in rule split_ccs in file /pasteur/appa/homes/aesposit/fiberseq-smk/workflow/rules/ccs.smk, line 85: Missing input files for rule split_ccs: output: temp/anna_sub_1/split_ccs/ccs.1-of-1.bam, temp/anna_sub_1/split_ccs/ccs.1-of-1.bam.pbi wildcards: sm=anna_sub_1, scatteritem=1-of-1 affected files: [path to bam file].pbi

I have pasted in the following text file the content of the ccs.smk, which seems to be the problem: ccssmk.odt

Thank you, and have a nice day!

mrvollger commented 2 months ago

We are no longer maintaining or supporting fiberseq-smk since this tool is now replaced by ft. You can read the readme of this repository and follow our quick start guide to learn about using ft https://fiberseq.github.io/quick-start.html