Troubleshooting

Installation of rsem hangs when using –use-conda

This is a known conda issue (#5536). One suggested solution is to remove the r channel from defaults in ~/.condarc:

default_channels:
- https://repo.continuum.io/pkgs/free
- https://repo.continuum.io/pkgs/pro

Also make sure your package order follows the ordering from bioconda:

channels:
  - bioconda
  - conda-forge
  - defaults

The workflow cannot find RSeQC or rpkmforgenes

Make sure you have created a conda environment for python2 packages whose name matches that of the configuration setting config[‘conda’][‘python2’] (default is py2.7).

STAR align cannot find the input files even though they are present

The input fastq file names depend on the configuration setting config[‘settings’][‘runfmt’] as well as config[‘ngs.settings’][‘read1_label’] (read2_label for read 2) and config[‘ngs.settings’][‘fastq_suffix’]. Make sure that read labels and fastq suffix are correctly configured.