Error in get_sampleReadsRaw_from_SeqLib(useSoftClippedBases = useSoftClippedBases

[John Lindo]

Hi Robert,

I'm trying to use STITCH on 37 Chimpanzee genomes but I'm getting a similar error as one of the previous posts but without the range issue. Please see below:

[2019-05-30 21:23:25] Error in get_sampleReadsRaw_from_SeqLib(useSoftClippedBases = useSoftClippedBases,  : 

  std::bad_alloc

Error in generate_input(bundling_info = bundling_info, L = L, pos = pos,  : 

  There has been an error generating the input. Please see error message above

Calls: STITCH -> generate_or_refactor_input -> generate_input

In addition: Warning message:

In mclapply(1:length(sampleRanges), mc.cores = nCores, FUN = loadBamAndConvert_across_a_range,  :

  scheduled cores 7, 2, 15, 8 encountered errors in user code, all values of the jobs will be affected

Execution halted

Any idea of what the problem might be?

Thank you!

Sincerely,

John 

[Robbie Davies]

Hey John,

I imagine this is a RAM issue (std::bad_alloc is a direct failure to allocate memory storage). Given the error message suggests >=15 cores are being used, can you try fewer cores and see if it works (otherwise keeping memory the same)? Alternatively, does it work on smaller regions (you can chunk the genome using regionStart, regionEnd and buffer). 

Also, is N=37 the total number? Just a warning that STITCH might perform modestly in this situation, it performs more optimally on larger N (i.e. > several hundred)

Best,

Robbie

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