Getting "Floating point exception (core dumped)" when running mauveAligner
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3.9 years ago
langziv ▴ 70

Hi.

When I run the following command I get a "Floating point exception (core dumped)":

/linux-x64/mauveAligner --output=/mauve/output.mauve --output-alignment=/mauve/output.alignment.

The bash script that calls the relevant python script:

#!/bin/bash
#PBS -q name
#PBS -N mauve
#PBS -e /err_and_out_files/mauve.ER
#PBS -o /err_and_out_files/mauve.OU
#PBS -l nodes=compute-0-311:ppn=10,mem=40000000kb

python "/scripts/mauve.py"

mauve.py:

import os
import shlex
import subprocess

directory = r'/output/mauve/'
mauve_path = "/mauve/linux-x64/mauveAligner"

for path in os.listdir(directory):
    file_name_A = os.path.basename(path)
    if 'A' in file_name_A:
        A_file = directory + file_name_A
        for file_name_B in os.listdir(directory):
            if 'B' in file_name_B:
                B_file = directory + file_name_B
                command = f'{mauve_path} --output={A_file[:-3]}_{file_name_B[:-3]}.mauve ' \
                          f'--output-alignment={A_file[:-3]}_{file_name_B[:-3]}.alignment'
                subprocess.run(shlex.split(command), capture_output=True).stdout.decode('utf-8')

I read the documentation and mauve-related questions and couldn't figure out what's wrong in the command.

Any ideas will be welcomed.

mauve mauveAligner floating-point-exception • 2.6k views
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Assuming this is related to your previous query where you're relying on loading via module, that would suggest you're in a HPC/scheduler type environment - are you requesting sufficient memory for the task to complete?

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I'm not sure. I'm adding the bash script in which there are various parameters, including memory usage.

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Try a smaller input dataset and request several GB of memory in the job submission script to ensure it completes. Your input dataset (without knowing anything about it) might be too large.

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The data sets are of whole assemblies. I'm not sure if I can break them into smaller files.

When I run the bash script there's no error file created. The error message I mentioned in the question appears when I run the command on a linux node. Actually, when I run the bash script an empty output file is created. The bash script calls a python script, from which mauve is called.

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How many assemblies? Just 2?

How big are the genomes?

You need to give us way more information, as a segfault is not a single issue with a single cause.

If you're running bash > bash script > python script you need to make sure the STDOUT and STDERR is captured correctly else the command may be failing 'silently' because the error isn't propagated correctly. I assume the bash script is the job submission file, why are you then calling a commandline program from python? Why not call it directly in the PBS script?

We need to see the content of /scripts/mauve.py

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Sorry about the delay. These are crazy days.

Yes. I'm runnnig 2 assemblies in every run. I just thought about it again, and I realize I can run multiple genomes to align with another genome, but since those are very big files, maybe I should stay with 2 genomes in every run.

The genomes' sizes are between 127 and 322 mb.

I wanted to call mauve from a python script so that I'll be able to iterate over multiple files. It can be done with bash, but I prefer doing it with python. I find python to be more convenient.

I'm adding the python script to the question.

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Those are very big sequences to align still. Mauve is a java tool if I recall, so you will need to ensure you're also passing flags to java to enable it to access more memory which it doesn't appear like you're doing.

I would imagine mauve simply doesn't have access to enough memory to complete the alignment correctly (since a segfault is generally a memory issue)

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The command I gave was inadequate. I didn't provide an sml file path. Once I did I managed to call mauve from a python script, but now I got a new issue. I'm getting the message: "* ERROR * Clust::SetLeafCount(0)" after mauve read the fasta files.

The command is

/mauveAligner --output=bwtrB2_btcaA1.mauve \
--output-alignment=bwtrB2_btcaA1.alignment \
/output/mauve/bwtrB2.fa /output/mauve/bwtrB2.sml \
/output/mauve/btcaA1.fa /output/mauve/btcaA1.sml`.

The printed output:

Sequence loaded successfully.
/output/mauve/bwtrB2.fa 280562226 base pairs.
Sequence loaded successfully.
/output/mauve/btcaA1.fa 130732691 base pairs.
Using weight 19 mers for initial seeds
Creating sorted mer list
Create time was: 144 seconds.
Creating sorted mer list
Create time was: 71 seconds.
0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..10%..
11%..12%..13%..14%..15%..16%..17%..18%..19%..20%..
21%..22%..23%..24%..25%..26%..27%..28%..29%..30%..
31%..32%..33%..34%..35%..36%..37%..38%..39%..40%..
41%..42%..43%..44%..45%..46%..47%..48%..49%..50%..
51%..52%..53%..54%..55%..56%..57%..58%..59%..60%..
61%..62%..63%..64%..65%..66%..67%..68%..69%..70%..
71%..72%..73%..74%..75%..76%..77%..78%..79%..80%..
81%..82%..v83%..vv84%..vvv85%..86%..87%..88%..89%..90%..
91%..92%..93%..94%..95%..96%..97%..98%..99%..Starting with 0 MUMs
Eliminating overlaps yields 0 MUMs

*** ERROR ***  Clust::SetLeafCount(0)
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