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mrmckain / Fast-Plast

Automated de novo assembly of whole chloroplast genomes.
MIT License
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Spades failed #39

Open jhcaddisfly opened 4 years ago

jhcaddisfly commented 4 years ago

Hi,

I try to run Fast-Plast as follows: perl /opt/Fast-Plast/fast-plast.pl -1 forward -2 reverse --name I30375 --bowtie_index Gentianales --coverage_analysis --clean light but apparently SPADES is not working proberly. I attached the error files. Could you please have a look?

Thanks, I30375_results_out.log I30375_Fast-Plast_Progress.log I30375_results_error.log

mrmckain commented 4 years ago

Hi,

There is a stack trace issue with SPAdes. I see you used bbnorm to correct your reads. If you check out the output here:

=== Stack Trace === [0x5f9c52] [0x58ada1] [0x55d191] [0x408c19] [0x40123c] [0x87b11b] [0x407c01] Verification of expression 'cov_.size() > 10' failed in function 'void coverage_model::KMerCoverageModel::Fit()'. In file '/spades/assembler/src/common/modules/coverage_model/kmer_coveragemodel.cpp' on line 187. Message 'Invalid kmer coverage histogram, make sure that the coverage is indeed uniform'. Verification of expression 'cov.size() > 10' failed in function 'void coverage_model::KMerCoverageModel::Fit()'. In file '/spades/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp' on line 187. Message 'Invalid kmer coverage histogram, make sure that the coverage is indeed uniform'. spades-core: /spades/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp:187: void coveragemodel::KMerCoverageModel::Fit(): Assertion `cov.size() > 10' failed.

You can see that the histogram of coverage is not uniform and throwing off spades. What type of data did you use here?

Best, Michael