I discovered something interesting and it could be a fact that has been known for some time regarding Konnector:
When running the following command after qlogin:
konnector -j 40 -k 96 -o kon96 out_reads_1.fastq out_reads_2.fastq
Konnector produces: kon96_reads1.fq, kon96_reads2.fq and kon96_pseudoreads.fa
If running konnector as a shell script it will not produce kon96_pseudoreads.fa but kon96_merged.fa.
This is an important difference because Konnector reads can be fed into Abyss-pe for finishing the genome assembly.