segment fault

[lingc31415]

Summary:

pyani v0.2.12, processing over 2,000 genome sequences reached out segmentation fault

Description:

I have dataset containing over 5,000 sequences. When Using pyani for pairwise ANI analysis, a segmentation fault occurs if the input dataset contains more than 2,000 sequences. however, it works well if I subset the dataset to contain fewer than 1,900 sequences.

Reproducible Steps:

average_nucleotide_identity.py
-i input_dir
-o output_dir_2
-m ANIm
-g
--gformat pdf
--write_excel
--worker 10

Current Output:

pop out segmentation fault. I guess it may be related to a deep or infinite recursion, where the stack space is exhausted.

Expected Output:

I wish it would work well with the entire dataset, but not just the subset dataset (>2,000 sequences).

pyani Version:

pyani v0.2.12

installed dependencies

If you are running a version of pyani v0.3 or later, then please run the command pyani listdeps at the command line, and enter the output below.

Python Version:

Python v3.12.2

Operating System:

Debian

[widdowquinn]

Hi @lingc31415 - thanks for using pyani.

Can you confirm that you are using multiprocessing to distribute jobs? And can you also provide the relevant section of the log file or error output, so we can see where in the analysis the failure happens?

Thanks,

L.

[widdowquinn]

Closed as pyani-plus is now preferred: https://github.com/pyani-plus/pyani-plus.