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troubleshooting.md

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Troubleshooting

Generic problems

Input files not found

If only no file, only one input file , or only read one and not read two is picked up then something is wrong with your input file declaration

  1. The path must be enclosed in quotes (' or ")
  2. The path must have at least one * wildcard character. This is even if you are only running one paired end sample.
  3. When using the pipeline with paired end data, the path must use {1,2} or {R1,R2} notation to specify read pairs.
  4. If you are running Single end data make sure to specify --singleEnd

If the pipeline can't find your files then you will get the following error

ERROR ~ Cannot find any reads matching: *{1,2}.fastq.gz

Note that if your sample name is "messy" then you have to be very particular with your glob specification. A file name like L1-1-D-2h_S1_L002_R1_001.fastq.gz can be difficult enough for a human to read. Specifying *{1,2}*.gz wont work give you what you want Whilst *{R1,R2}*.gz will.

The above information is also covered in the usage README.

Some of my samples are missing!

If the pipeline ran without crashing and some samples are missing then there are two possible explanations:

  1. You made a mistake when declaring the input files - in that case see above.

Extra resources and getting help

If you still have an issue with running the pipeline then feel free to contact us: UCL-BLIC website.