Troubleshooting¶
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.