I tried to a short test run with "real" data using the most recent sebhtml/ray git, and got the following error: Rank 0 has 4463742 k-mers (completed)
Rank 0: the minimum coverage is 1 Rank 0: the peak coverage is 1 Rank 0: Assembler panic: no peak observed in the k-mer coverage distribution. Rank 0: to deal with the sequencing error rate, try to lower the k-mer length (-k) Rank 0: sent 241979 messages, received 241978 messages. I get the same outcome with my 5k phix assembly test: $ ../../../sebgit/ray/code/Ray -p tests/phix/phix_5k_1.fasta tests/phix/phix_5k_2.fasta ... Rank 0 has 10466 k-mers (completed) Rank 0: the minimum coverage is 1 Rank 0: the peak coverage is 1 Rank 0: Assembler panic: no peak observed in the k-mer coverage distribution. Rank 0: to deal with the sequencing error rate, try to lower the k-mer length (-k) Rank 0: sent 201223 messages, received 201222 messages. When this happened previously, I managed to get around it by re-writing the smoothing function (https://github.com/gringer/ray/commit/f048203e571d4c7a267dace27fec063cfe2059dd), but you're no longer using a separate smoothing function in your coverage analysis code. Why are these assemblies failing? The data I'm working from is here: http://user.interface.org.nz/~gringer/hacking/planaria_454.fasta [about 7MB] http://user.interface.org.nz/~gringer/hacking/phix_5k_1.fasta [about 300kB] http://user.interface.org.nz/~gringer/hacking/phix_5k_2.fasta [about 300kB] Cheers, David ------------------------------------------------------------------------------ 5 Ways to Improve & Secure Unified Communications Unified Communications promises greater efficiencies for business. UC can improve internal communications as well as offer faster, more efficient ways to interact with customers and streamline customer service. Learn more! http://www.accelacomm.com/jaw/sfnl/114/51426253/ _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
