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bioinfologics / satsuma2

FFT cross-correlation based synteny aligner, (re)designed to make full use of parallel computing
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Segmentation fault #24

Open Lutri22 opened 4 years ago

Lutri22 commented 4 years ago

Hi,

I am trying to run Satsuma2 which was installed used by conda. It is running for a while but then I got the following error:

Loading fasta Loading fasta S18_corrected_scaffolded_final.fasta into kmer array LrA_corrected_scaffolded_final.fasta into kmer array Kmer array with 790085333 elements created TIME_LOG: 1574890330696 - Sorting array Kmer array with 832860422 elements created TIME_LOG: 1574890332056 - Sorting array Kmer array sorted Kmer array filtered to 580142123 elements Kmer array sorted Kmer array filtered to 652365840 elements Starting to create matching positions 34916694 matching positions Sorting the matches Dumping matches of 1 kmers with jumps of up to 30kmers to Lr_satsuma_test/kmatch_results.k31 3033606 matches dumped Waiting for seed pre-filters... loading results for k=11 Segmentation fault

My command was the following: SatsumaSynteny2 -t S18_corrected_scaffolded_final.fasta -q LrA_corrected_scaffolded_final.fasta -o Lr_satsuma_test -t 12 Could you please help me solve this problem?

Many Thanks,

Szabolcs

Lutri22 commented 4 years ago

I tried to install it using CMake but I am still getting the same error.