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nf-core/lncpipe: Troubleshooting

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.

Data organization

The pipeline can't take a list of multiple input files - it takes a glob expression. If your input files are scattered in different paths then we recommend that you generate a directory with symlinked files. If running in paired end mode please make sure that your files are sensibly named so that they can be properly paired. See the previous point.

Extra resources and getting help

If you still have an issue with running the pipeline then feel free to contact us. Have a look at the pipeline website to find out how.

If you have problems that are related to Nextflow and not our pipeline then check out the Nextflow gitter channel or the google group.

Tips & FAQs

Tips

  • 😊Plz keep the consistency of your genome sequence, index library and annotation files: genome version, chromosome format, gtf coordinated e.g. The third-party software may stop for any of the above reasons.
  • 😕Setting your analysis parameters always in config file, differ project should corresponding to differ configurations for reproductive analysis. To rerun a project, you can just specify -c your.config in your command, which can also help you to record analysis parameters.
  • 😮Run analysis on docker container, no much to say.
  • 😬Always use the latest version to be away from the known bugs.

FAQ

In local mode:

  • 1. PLEK throws an error "/data/software/PLEK.1.2/PLEK.py:line12: $'\r': can not find command", how to fix?

A: using the follow command as suggested in the installation section.

    perl -CD -pi -e'tr/\x{feff}//d && s/[\r\n]+/\n/' *.py
  • 2. IOError: [Errno 2] No such file or directory: '/opt/CPAT-1.2.3/dat/Human_Hexamer.tsv'?

A: The cpat command required the Human_Hexamer.tsv to predict lncRNA coding potential, plz check your cpatpath parameters.

  • 3. When using htseq to quantify transicript, it throws "Error occured when reading beginning of SAM/BAM file. 'csamtools.AlignedRead' object has no attribute 'reference_start' "

A: It's a version conflict caused by htseq and hisat generated bamfile, a possible solution for this is to install the old version of htseq