Anton Korobeynikov
Anton Korobeynikov
Unfortunately, this is a known problem with CQF implementation we're using. There is no workaround currently. You may try to quality trim your read and run --only-assembler
@alienzj Sure, patches are welcome!
"counting quotient filter"
Hello Thank you for your interest in SPAdes. Please attach the files that were mentioned just two lines below the ones you copied (and before the gihub link).
How much free RAM is available for your SPAdes job?
The log reads: ``` spades-core: /usr/local/src/SPADES/SPAdes-3.12.0/src/common/sequence/sequence.hpp:70: void Sequence::InitFromNucls(const S&, bool) [with S = std::__cxx11::basic_string]: Assertion `is_dignucl(s[0]) || is_nucl(s[0])' failed. ``` So it seems you're having non-ACTGN symbols in your contig...
Hello Will it be possible to upload your spades.log file?
Looks like one of the files got truncated, probably during the gzip compression – the number of reads written by BayesHammer and the number of reads received by SPAdes differ.
Will you please provide spades.log and params.txt files as you were instructed in the error message?
@wuinqing @parulbaranwal Please do not hijack other issues and open new ones using the instructions provided. Thanks!