BFAST malloc error

CS Student

Member

Join Date: Apr 2011

Posts: 20
- Share
- Tweet
#1

BFAST malloc error

01-11-2012, 12:12 PM

Hi,

I am getting the below memory corruption error when trying to run BFAST on a 4GB RAM machine.

Could you please advise?

Thanks.
=========================================

*** glibc detected *** bfast: malloc(): memory corruption: 0x097f80a8 ***
======= Backtrace: =========
/lib/i686/nosegneg/libc.so.6[0x472dbc]
/lib/i686/nosegneg/libc.so.6(__libc_malloc+0x85)[0x473f95]
/lib/i686/nosegneg/libc.so.6(vasprintf+0x23)[0x469753]
/lib/i686/nosegneg/libc.so.6(asprintf+0x2e)[0x44f03e]
/lib/i686/nosegneg/libc.so.6(__assert_fail+0xba)[0x42b2ba]
bfast[0x8062baa]
bfast[0x8064080]
bfast[0x806f4d5]
bfast[0x8071038]
bfast[0x8078470]
bfast[0x807d7ef]
/lib/i686/nosegneg/libc.so.6(__libc_start_main+0xdc)[0x41edec]
bfast[0x8049421]
======= Memory map: ========
003eb000-00405000 r-xp 00000000 ca:01 526533 /lib/ld-2.5.so
00405000-00406000 r-xp 00019000 ca:01 526533 /lib/ld-2.5.so
00406000-00407000 rwxp 0001a000 ca:01 526533 /lib/ld-2.5.so
00409000-00549000 r-xp 00000000 ca:01 526534 /lib/i686/nosegneg/libc-2.5.so
00549000-0054b000 r-xp 00140000 ca:01 526534 /lib/i686/nosegneg/libc-2.5.so
0054b000-0054c000 rwxp 00142000 ca:01 526534 /lib/i686/nosegneg/libc-2.5.so
0054c000-0054f000 rwxp 0054c000 00:00 0
00557000-0057c000 r-xp 00000000 ca:01 526536 /lib/i686/nosegneg/libm-2.5.so
0057c000-0057d000 r-xp 00024000 ca:01 526536 /lib/i686/nosegneg/libm-2.5.so
0057d000-0057e000 rwxp 00025000 ca:01 526536 /lib/i686/nosegneg/libm-2.5.so
00580000-00593000 r-xp 00000000 ca:01 526543 /lib/i686/nosegneg/libpthread-2.5.so
00593000-00594000 r-xp 00012000 ca:01 526543 /lib/i686/nosegneg/libpthread-2.5.so
00594000-00595000 rwxp 00013000 ca:01 526543 /lib/i686/nosegneg/libpthread-2.5.so
00595000-00597000 rwxp 00595000 00:00 0
005fb000-0060d000 r-xp 00000000 ca:01 693408 /usr/lib/libz.so.1.2.3
0060d000-0060e000 rwxp 00011000 ca:01 693408 /usr/lib/libz.so.1.2.3
0061b000-00626000 r-xp 00000000 ca:01 526548 /lib/libgcc_s-4.1.2-20080102.so.1
00626000-00627000 rwxp 0000a000 ca:01 526548 /lib/libgcc_s-4.1.2-20080102.so.1
00648000-00658000 r-xp 00000000 ca:01 700448 /usr/lib/libbz2.so.1.0.3
00658000-00659000 rwxp 0000f000 ca:01 700448 /usr/lib/libbz2.so.1.0.3
08048000-08094000 r-xp 00000000 ca:01 692332 /usr/local/bin/bfast
08094000-08096000 rwxp 0004b000 ca:01 692332 /usr/local/bin/bfast
097ed000-0985f000 rwxp 097ed000 00:00 0
aff00000-aff21000 rwxp aff00000 00:00 0
aff21000-b0000000 ---p aff21000 00:00 0
b0003000-b2004000 rwxp b3f8a000 00:00 0
b204a000-b7fa1000 rwxp b204a000 00:00 0
b7fa5000-b7fa9000 rwxp b7fa5000 00:00 0
b7fa9000-b7faa000 r-xp b7fa9000 00:00 0 [vdso]
bfba6000-bfbbb000 rw-p bfba6000 00:00 0 [stack]
Tags: None
nilshomer

Nils Homer

Join Date: Nov 2008

Posts: 1283
- Share
- Tweet
#2

01-11-2012, 06:16 PM

Could you try to find a small test case so we can debug, or run it in gdb and identify the line in the source code? Tell us your environment and other variables.
Comment

Previous template Next

Nine Things a Sample Prep Scientist Thinks About Before Sequencing

by SEQadmin2

I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.

Here are nine questions we think about, in roughly the order they matter, before...
- Channel: Articles
Today, 07:11 AM
From Collection to Sequencing: Why Sample Preparation and Preservation Define Sequencing Data

by SEQadmin2

Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.

The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...
- Channel: Articles
06-02-2026, 10:05 AM
Single-Cell Sequencing at an Inflection Point: Early Impacts of New Platforms and Emerging Trends

by SEQadmin2

With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.

Introduction

Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...
- Channel: Articles
05-22-2026, 06:42 AM

Topics	Statistics	Last Post
Whole-Genome Sequencing Traces Faroe Islands Ancestry to a North Atlantic Founder Population by SEQadmin2 Started by SEQadmin2, Yesterday, 06:09 AM	0 responses 16 views 0 reactions	Last Post by SEQadmin2 Yesterday, 06:09 AM
Sequencing the Two-Toed Sloth Genome Reveals Jumping Genes Tied to Its Extreme Metabolism by SEQadmin2 Started by SEQadmin2, 06-09-2026, 11:58 AM	0 responses 37 views 0 reactions	Last Post by SEQadmin2 06-09-2026, 11:58 AM
A New Method Makes Hantavirus Genome Analysis Faster and More Accessible by SEQadmin2 Started by SEQadmin2, 06-05-2026, 10:09 AM	0 responses 42 views 0 reactions	Last Post by SEQadmin2 06-05-2026, 10:09 AM
A New Single-Cell Method Maps DNA-Protein Interactions by SEQadmin2 Started by SEQadmin2, 06-04-2026, 08:59 AM	0 responses 49 views 0 reactions	Last Post by SEQadmin2 06-04-2026, 08:59 AM

Unconfigured Ad

Comment

Latest Articles

ad_right_rmr

News