Hi! I'm running the abyss-pe script with the 'long' parameter to enable rescaffolding of my assembly with longer contigs. Unfortunately, the process stops at this very step. The problem is most likely related to the 'bwa mem' command. When comparing how abyss-pe executed 'bwa mem' with what the command is supposed to look like, I see that one of the input files is missing.

bwa mem -a -t24 -S -P -k63 myassembly_k63-8.fa  \
        |gzip >../long_contigs.fasta-8.sam.gz
bwa mem -a -t$j -S -P -k$l $(name)-8.fa $(strip $($*)) \
        |gzip >$@

As you can see, the following fragment of the code $(strip $($*)) returns nothing and due to insufficient number of input parameters, the 'bwa mem' exits:

Usage: bwa mem [options] <idxbase> <in1.fq> [in2.fq]