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.