Hello! I've got to run abyss-pe on 2 files I've got and find the best parameters (k and so on) that would create the best contig coverage (sorry if I'm messing things up, I'm a programmer that had a short bioinformatics crash course). The files I've got are paired end reads of the Clorella Variabilis chloroplast and each take 304MB.
This is my run command
abyss-pe k=25 n=10 v=-v c=118 e=51 name=test in='reads1.fastq reads2.fastq'
Since I run the program on verbose and see a memory load I think that this is not a RAM issue (I have 16GB of ram on the system). I've tried running the fastQValidator tool and it said the files seem to be invalid, however my lecturer assures me they are valid and in fact paired ends. The files are in FASTQ format (I guess created on a Illumina/Sanger machine) so they contain some strange characters like scopes and non-ACGT characters in the quality strings and the sequence it self.
this is where the progress stops:
Mapped 1432486 of 1481614 reads (96.7%) Mapped 1430166 of 1481614 reads uniquely (96.5%) Read 1481614 alignments Mateless 1481614 100% Unaligned 0 Singleton 0 FR 0 RF 0 FF 0 Different 0 Total 1481614 abyss-fixmate: error: All reads are mateless. This can happen when first and second read IDs do not match. error: `test-3.hist': No such file or directory
The link I'm submitting contains the whole output during the runtime of abyss-pe in verbose mode.
I've tried all I could (or know for that matter - since it is a crash course for software engineers I took as a diversity course during my BSc), I'd appreciate some help. Thanks ahead!