lognumslots.sh sometimes underestimates the required number of slots about squeakr HOT 2 OPEN

Hi @hmusta , in the current version of Squeakr, we have auto-resizing when running with a single thread. So, even if you underestimate the size there won't be a seg fault. Please try it and let me know if you still have any issues.

Thanks,
Prashant

from squeakr.

Hello,

i observed segfaults when using the value from lognumslots.sh as well, with the squeakr version from Oct 2019 (should be 5ad2ad6).

This seems to happen frequently for me on very small test datasets.

Reproducing this should be quite simple:

Create a file (called 1.fastq) containing:

@1_1/1
TATGCACCAGAGTATGGAAGCATAAGCTCTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCAGTCAACAAAGCCGAGTGGGCGCAACGA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

Then run ntcard followed by lognumslots.sh:

ntcard -k32 1.fastq -p ntcard.out
lognumslots.sh ntcard.out_k32.hist

lognumslots returns 7, but the smallest value for which squeakr count doesn’t crash is 10.

squeakr count -n -e -k 32 -s 7 -o 1.squeakr 1.fastq

results in a seqfault, while

squeakr count -n -e -k 32 -s 10 -o 1.squeakr 1.fastq

works fine.

from squeakr.