Comments (2)
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
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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 doesnโt 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.
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