Hi there,

I am running a GWAS analysis with SNPTEST, SNPTEST runs for about a minute and then stops and memory dumps. I have run this analysis on these exact file previously but I added in an extra covariate to the phenotype file.

The error I am getting is as follows:

scanning... read chunk [250 of (unknown)]... done. scanning... read chunk [251 of (unknown)]...snptest_v2.5.2: ../statfile/include/statfile/StatSink.hpp:94: statfile::StatSink<t1, t2,="" t3,="" t4,="" t5,="" t6,="" t7,="" t8,="" t9,="" t10="">& statfile::StatSink<t1, t2,="" t3,="" t4,="" t5,="" t6,="" t7,="" t8,="" t9,="" t10="">::operator<<(const statfile::EndRow&) [with T1 = genfile::MissingValue, T2 = long unsigned int, T3 = int, T4 = unsigned int, T5 = long int, T6 = long unsigned int, T7 = std::basic_string<char>, T8 = double, T9 = genfile::Chromosome, T10 = genfile::GenomePosition, statfile::StatSink<t1, t2,="" t3,="" t4,="" t5,="" t6,="" t7,="" t8,="" t9,="" t10=""> = statfile::StatSink<genfile::missingvalue, long="" unsigned="" int,="" int,="" unsigned="" int,="" long="" int,="" long="" unsigned="" int,="" std::basic_string<char="">, double, genfile::Chromosome, genfile::GenomePosition>]: Assertion `m_current_column == number_of_columns()' failed. ./Script_SNPTEST.sh: line 3: 144880 Aborted (core dumped)

I have tried changing the phenotype file but am still getting the same error. Has anyone seen an error like this previously?

Any help would be greatly appreciated!

Many thanks,

Caragh