I'm having trouble getting scythe and qrqc to play nice together. The trimmed fastq from scythe throws a segfault when loaded into qrqc. The untrimmed fastq file loads and summarizes fine. It is only the scythe trimmed file that is throwing a segfault, not the initial untrimmed reads. Any ideas about what is causing this? I tried hash=FALSE as well. I'm confused because these seem to be part of a Galaxy pipeline. Here's what I did:
From the command line:
scythe -a illumina_adapters.fa -o scythe_file.fastq -m matches.txt -q sanger raw.fastq
Hey Vince,
I'm having trouble getting scythe and qrqc to play nice together. The trimmed fastq from scythe throws a segfault when loaded into qrqc. The untrimmed fastq file loads and summarizes fine. It is only the scythe trimmed file that is throwing a segfault, not the initial untrimmed reads. Any ideas about what is causing this? I tried hash=FALSE as well. I'm confused because these seem to be part of a Galaxy pipeline. Here's what I did:
From the command line:
scythe -a illumina_adapters.fa -o scythe_file.fastq -m matches.txt -q sanger raw.fastq
Then in R:
readSeqFile(file=scythe_file,type="fastq",quality="sanger")
And here's the segfault
* caught segfault * address 0x1057eb000, cause 'memory not mapped'
Traceback: 1: .Call("summarize_file", filename, as.integer(max.length), as.integer(qtype), as.logical(hash), as.numeric(hash.prop), as.logical(kmer), as.integer(k), as.logical(verbose)) 2: readSeqFile(file = scythe_file, type = "fastq", quality = "sanger")
I'm working from a macbook laptop Mac OSX 10.6.8 with 8GB memory.
Thanks so much for any help you can provide!