Anton Korobeynikov
Anton Korobeynikov
Ok, does the assembly finish if you'd use `--only-assembler` option in addition to yours?
No, there are no "conflicts". Likely the problem will be solve if you'd compile SPAdes for the host machine instead of using pre-built binaries.
@sxh1136 Thanks. I assigned the issue to metaplasmidSPAdes leading author. Note that the tool was never included into any SPAdes release
Will you please post your spades.log file?
Please rerun just SPAdes and check whether the warnings are still there. But these ones are not benign and might indicate suboptimal assembly.
There might be multiple sources of problems: * Issues with the input data (e.g. uneven coverage or coverage gap) * Aggressive processing of Shovil (that could lead to coverage gaps,...
will you please attach your spades.log files?
Hello Please provide us your spades.log file
This smells like an I/O issue. Does the problem reproduce if you'd simply restart everything from scratch?
> According to our discussion, could it mean it is almost impossible to produce scaffolds from the assembled contigs? Well, the situation with SPAdes is quite the opposite. contigs are...