qAlign fails when run with a cluster object if no reads align

[csoneson]

(Moving here from slack)

Setting:

• paired-end RNA-seq data
• aligning against a short reference with bowtie
• using a cluster object
• not including unmapped reads in the sam/bam file
• for some samples, no reads align

What happens:
QuasR::qAlign() gives an error:

Error in checkForRemoteErrors(val) : 
  one node produced an error: Error on ***** processing sample *****.fastq : second argument must be a list

According to the log file, the error appears in the sam to bam conversion step.
If run without the cluster object, it runs without errors and produces an empty sam file.