Anton Korobeynikov
Anton Korobeynikov
Hello It does not look like a metagenomic dataset: it is very small (both in terms of # of reads and the genome size), however the average coverage is very...
The answer is easy - SPAdes does not decide anything. The amount of RAM required depends on your input dataset, coverage, error rate, repeat content, etc. In general we cannot...
Tom, the description of the problem was given above. At the time of error SPAdes had ~ 120 Gb of RAM allocated, however, your OS failed to fulfill SPAdes' request...
There might be multiple issues starting from virtual memory fragmentation and ending with memory overcommit by other apps. You may want to ask your system administrator how the particular server...
Depends on the stage of the process. Some stages require fixed amount of RAM per thread (however, we try to estimate the amount of free memory depending on the specified...
Hello. Sorry, it seems that library are counted from 0 there. So, in this particular case these are libraries 1 and 5. What is the size of `/media/bigdrive1/sam/Spirochete_Project/All_Spades_Assembly/corrected/003D_200bp_lib0_1.cor.fasta` and `/media/bigdrive1/sam/Spirochete_Project/All_Spades_Assembly/corrected/003B_200bp_lib4_1.cor.fasta`?
And what is inside?
Well, it may happen that one library could cause others to appear completely "bad", but still this is something pretty unexpected. IonTorrent handling code did not change over last 5-6...
Does the problem reproduce if you'd restart failed SPAdes job? If you'd change the # of threads used?
Hello Please attach the spades.log file from this run.