I'm attempting to do de novo hybrid assemblies with paired-end illumina data and PacBio long-read data using SPAdes (3.5.0 Darwin, on OSX 10.10.3). I have 11 different bacteria species, all of which were sequenced the same way at the same time. For some of these species, the assembler runs through perfectly (using default parameters), so I believe I've got it set up correctly, but for some of them, it runs through most of the process and then spits an error code:
== Error == system call for: "['home/path/SPAdes-3.5.0-Darwin/bin/spades', 'project/path/K55/configs/config.info']" finished abnormally, err code: -10
This occurs near the end of the k55 assembly step. I can't find anything obviously different between the samples that work and the samples that don't, and can't find any documentation on this particular error code. Can anyone help figure out what the problem is/figure out a fix?