Anton Korobeynikov
Anton Korobeynikov
Well, the real reason is that you're assembling reads with highly uneven coverage in isolate mode that expects even. So, lots of different problems could appear here as SPAdes certainly...
Oh, and given the # of reads, I doubt that `--cov-cutoff 8` is what you want. If you found this assembly "recipe" somewhere, I think you need to tune it...
I doubt that the contigs are "spurious". They do exist in your input data :)
@russellj7 This smells very strange and indicates some sort of corruption somewhere. Does changing the number of threads work?
It smells like some bug around memory allocation on Mac OS, frankly speaking...
Hello It's highly likely that your input reads are corrupted, e.g. the length of the sequence line do not correspond to the length of quality line in FASTQ
Hello Thank you for your interest in SPAdes. > I got "Segmentation fault (core dumped)" message at bwa mem alignment step (the last few lines copied below my message and...
So far the only workaround is to recompile SPAdes from source. Will be an option for you?
Just take the latest released version. You need to modify https://github.com/ablab/spades/blob/spades_3.13.1/assembler/src/projects/corrector/dataset_processor.cpp#L139 Just change "is" to "auto" there and recompile.
@davidbio Please do not hijack other issues even if there are some similar words, the sources of problems might be completely different :) Please check whether the latest SPAdes 3.13...