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Maximum number of contigs in a simulation #2320
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Hi @teng-gao, can you attach your file |
Hello @marehr , I think I met a similar problem. The command I used is:
The error I got is: MASON SIMULATORINITIALIZING__________________________________________________________ Opening reference and variants file ... OK The reference data I used is from: Thank you! |
Mason seems to open a file handle for each fragment. The default limit is usually If I increase my limit to Note: The file handle situation is a recurring problem with Mason. However, deferring the opening of the handles, i.e. only opening them when actually needed, would require a major restructuring of the code, which is not feasible for us. Hence, we focus on properly documenting the bahavior and adding checks with useful error output. |
Thank you for the answer! It works. |
@SGSSGene were there any reasons to reopen this ticket? Thank you. |
It seems mason_simulator crushes if there are >150 contigs in the fasta file.
mason_simulator -ir myfasta.fa -n 5000 -o left.fq -or right.fq
Error message:
MASON SIMULATOR
INITIALIZING__________________________________________________________
Opening reference and variants file ... OK
Initializing fragment-to-contig distribution ... OK
Initializing simulation threads ... OK
Opening output file left.fq ... OK
Opening output file right.fq ...Abort trap: 6
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