Anton Korobeynikov
Anton Korobeynikov
Please attach the file itself
I cannot reproduce the problem, everything is ok for me. So, likely there is some local problem. In any case, these reads are not valid SPAdes input as Illumina reads...
Per SPAdes manual (https://ablab.github.io/spades/input.html): To run SPAdes you need at least one library of the following types: - Illumina paired-end/high-quality mate-pairs/unpaired reads - IonTorrent paired-end/high-quality mate-pairs/unpaired reads - PacBio CCS...
Assigning to metaviralSPAdes author
Your SPAdes job seems to be externally killed in "110 Gb" case. Are you also setting any memory limits / quotas on your cluster via some job submission script?
The place where is crashed does not allocate much memory at all. Sometimes clusters impose memory limits per core and this might influence with memory allocation
As far as I can see, it consumes ~6 Gb. Due to memory allocation overhead, etc. this means that the memory allocator could request from OS a bit more. Which...
> Ok, I hadn't realised the memory logs were meant to be reporting usage per thread. They are not. However oftentimes various job schedulers assumes memory per thread, etc. and...
Tagging @Itolstoganov - cloudSPAdes author
Unfortunately, we cannot change the license of SPAdes as SPAdes team does not hold copyright on the code. We are not lawyers as well, so we cannot speak about GPLv2...