Getting 'Bus Error: 10' When Running The Prody Package On A Multiple Sequence Alignment
1
0
Entering edit mode
11.1 years ago
Harpalss ▴ 310

I am using the prody package to do some co-evolution analysis on my multiple sequence alignment (MSA).

When I parse the MSA file using prody I get a Bus error: 10

Code:

from prody import *
msa = parseMSA('test_aln.fasta')

This outputs the following in my terminal:

>>> from prody import *
>>> msa = parseMSA('cbpa_aln.fasta')
Bus error: 10

I can't figure out why i am getting this error. I've tried restarting my machine and re-installing prody but to no avail.

Test Data:

>CbpA
--------------------------------------------------
------------ASALKDYYAIMGVKPTDDLKTIKTAYRRLARKYHPDVS
KEP---DAEARFKEVAEAWEVLSDEQ--RRAEYDQMWQH---RN-DP--Q
FNRQFHHGDG----------------------------------------
---------QSFNAEDFDDIFSSIFGQHA----RQ---------------
---------------SRQRPATRGHDIEIEVAVFLEETLTEHKRTISYNL
PVYNA-FG---------------MIEQEIPKTLNVKIPAGVGNGQRIRLK
GQGTPGENG-----GPNGDLWLVIHIAPHPL-FDIVGQDLEIVVPVSPWE
AALGAKVTVPTLK-ESILLTIPPGSQAGQRLRVKGKGLVSK---KQT--G
DLYAVLKIVMPPKP-DENTAALWQQLADAQSSFDPRKDWGKA--------
---
>gi|422828735|ref|ZP_16876905.1|
--------------------------------------------------
-------------MELKDYYAIMGVKPTDDLKTIKTAYRRLARKYHPDVS
KEP---DAEARFKEVAEAWEVLSDEQ--RRAEYDQMWQH---RN-DP--Q
FNRQFHHGDG----------------------------------------
---------QSFNAEDFDDIFSSIFGQHA----RQ---------------
---------------SRQRPATRGHDIEIEVAVFLEETLTEHKRTISYNL
PVYNA-FG---------------MIEQEIPKTLNVKIPAGVGNGQRIRLK
GQGTPGENG-----GPNGDLWLVIHIAPHPL-FDIVGQDLEIVVPVSPWE
AALGAKVTVPTLK-ESILLTIPPGSQAGQRLRVKGKGLVSK---KQT--G
DLYAVLKIVMPPKP-DENTAALWQQLADAQSSFEPRKDWGKA--------
---
python • 3.2k views
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2
Entering edit mode
11.1 years ago

A bus error usually indicates a programming error that most likely comes from a section of the code that was written in C and it has to do with memory access/management.

It is a serious and unrecoverable error that you probably cannot solve on your own. You should contact the developer.

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