Problems with README and runDisco.sh?

I am trying to get Disco running. Apart from this issue, in following the README I have two questions on the section under quickly running the assembler.

first, what is ${OP_PREFIX}? can it be arbitrary? I set it to xxx.
when I run runDisco it seems like things must be fail well before the error message :)

./runDisco.sh -d podar -inP SRR606245.pe.qc.fq.gz -n 8 -o xxx
Graph construction module ./buildG exists.
Partial graph simplification module ./parsimplify exists.
Graph simplification module ./fullsimplify exists.
Cresting output directory: podar
Starting Time is Mon Jun 5 14:28:14 EDT 2017
cat: podar/assembly/xxx_contigsFinal_*.fasta: No such file or directory
cat: podar/assembly/xxx_scaffoldsFinal_*.fasta: No such file or directory
Ending Time is Mon Jun 5 14:28:15 EDT 2017

the log file indicates that the file didn't exist (which was my fault - a faulty ln -s) but it seems like runDisco should exit on this kind of failure!

>>> Function start: loadReadLenghtsFromReadFile()
load reads from read file: SRR606245.pe.qc.fq.gz
         0 read lengths loaded from this read file
<<< Function stop: loadReadLenghtsFromReadFile(), Elapsed time: 9.93079e-05 seco
nds, Memory usage: 1 - 1 = 0 MB.
----
<<< Function stop: DataSet(), Elapsed time: 0.000196602 seconds, Memory usage: 1
 - 1 = 0 MB.

also, 'seperately' is misspelled.

I think 'mate pairs' is an incorrect specification in Illumina - generally we use 'mate pair' for long-insert paired reads, and 'paired end' for short-insert/standard illumina.

abiswas-odu / Disco

Problems with README and runDisco.sh? #4