Generate allele count error

[John Joseph]

Hi there!

Seeing the following error:

244 [2024-02-09 21:18:03] downsample sample AV-1-4-13_AV-1-4-13 - 1960806 of 4767649 reads removed
   245 [2024-02-09 21:18:11] Done generating inputs
   246 [2024-02-09 21:18:11] Copying files onto tempdir
   247 [2024-02-09 21:33:53] Done copying files onto tempdir
   248 [2024-02-09 21:33:53] Generate allele count
   249 [2024-02-09 21:48:25] Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
   250
   251 Error in check_mclapply_OK(out2) :
   252   An error occured during STITCH. The first such error is above
   253 Calls: STITCH -> buildAlleleCount -> check_mclapply_OK
   254 In addition: Warning messages:
   255 1: In mclapply(1:length(sampleRanges), mc.cores = nCores, FUN = loadBamAndConvert_across_a_range,  :
   256   scheduled core 7 did not deliver a result, all values of the job will be affected
   257 2: In mclapply(sampleRanges, mc.cores = nCores, FUN = buildAlleleCount_subfunction,  :
   258   scheduled core 7 encountered error in user code, all values of the job will be affected
   259 Execution halted

I've tried various memory and cpus configurations.

Additional problem: The downsampling phase starts off taking advantage of the cores that are allocated to it and moving quite quickly. By the end of the downsampling phase, Stitch is only using one core and moving very slowly.

Any suggestions on either of these issues would be greatly appreciated! Thank you!

[John Joseph]

I was watching htop to see what was going on when the error occurs. I didn't see a peak in memory usage. The last command I saw was deleting the tmp directory and then the error hit.

[John Joseph]

My issue appears to be similar to https://groups.google.com/g/stitch-imputation/c/6nZLlAl3c4E except I do not have the memory not mapped error(*** caught segfault ***address 0xd4d11000, cause 'memory not mapped').