genomeCoverageBed error/bug?

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Jamie Walters

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Mar 23, 2012, 2:54:29 AM3/23/12
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Okay, I've got an error here that I cannot understand. running
v2.16.1

I sorted my bamfile with samtools sort.

I think I've got my .genome file straight (worked OK with
complementBed).

$ head Hmel_genome_sorted.bed
scf7180000006000 83500
scf7180000006004 223569
scf7180000006013 163478
scf7180000006014 174540
scf7180000006016 353155
scf7180000006018 238359
scf7180000006022 177333


but I repeatedly get the same type of error with different bam
files...

Is this a bug, or am I doing something wrong?

Thanks!

jamie

++++++++++++++++++++++++

$genomeCoverageBed -ibam sorted.test.bam -g Hmel_genome_sorted.bed >
out

*** glibc detected *** bedtools: free(): invalid next size (fast):
0x0000000000a31ea0 ***
======= Backtrace: =========
/lib/libc.so.6(+0x775b6)[0x7f88c75ad5b6]
/lib/libc.so.6(cfree+0x73)[0x7f88c75b3e83]
bedtools[0x460218]
bedtools[0x4601fc]
bedtools[0x45c46e]
bedtools[0x461b5e]
bedtools[0x4368ab]
/lib/libc.so.6(__libc_start_main+0xfd)[0x7f88c7554c4d]
bedtools[0x406d89]
======= Memory map: ========
00400000-00546000 r-xp 00000000 08:03
12716876 /disk1/jw663/src/BEDTools-
Version-2.16.1/bin/bedtools
00746000-00748000 r--p 00146000 08:03
12716876 /disk1/jw663/src/BEDTools-
Version-2.16.1/bin/bedtools
00748000-00749000 rw-p 00148000 08:03
12716876 /disk1/jw663/src/BEDTools-
Version-2.16.1/bin/bedtools
00749000-0074a000 rw-p 00000000 00:00 0
00868000-00a4f000 rw-p 00000000 00:00
0 [heap]
7f88c0000000-7f88c0021000 rw-p 00000000 00:00 0
7f88c0021000-7f88c4000000 ---p 00000000 00:00 0
7f88c7536000-7f88c76b0000 r-xp 00000000 08:21
786785 /lib/libc-2.11.1.so
7f88c76b0000-7f88c78af000 ---p 0017a000 08:21
786785 /lib/libc-2.11.1.so
7f88c78af000-7f88c78b3000 r--p 00179000 08:21
786785 /lib/libc-2.11.1.so
7f88c78b3000-7f88c78b4000 rw-p 0017d000 08:21
786785 /lib/libc-2.11.1.so
7f88c78b4000-7f88c78b9000 rw-p 00000000 00:00 0
7f88c78b9000-7f88c78cf000 r-xp 00000000 08:21
786487 /lib/libgcc_s.so.1
7f88c78cf000-7f88c7ace000 ---p 00016000 08:21
786487 /lib/libgcc_s.so.1
7f88c7ace000-7f88c7acf000 r--p 00015000 08:21
786487 /lib/libgcc_s.so.1
7f88c7acf000-7f88c7ad0000 rw-p 00016000 08:21
786487 /lib/libgcc_s.so.1
7f88c7ad0000-7f88c7b52000 r-xp 00000000 08:21
786792 /lib/libm-2.11.1.so
7f88c7b52000-7f88c7d51000 ---p 00082000 08:21
786792 /lib/libm-2.11.1.so
7f88c7d51000-7f88c7d52000 r--p 00081000 08:21
786792 /lib/libm-2.11.1.so
7f88c7d52000-7f88c7d53000 rw-p 00082000 08:21
786792 /lib/libm-2.11.1.so
7f88c7d53000-7f88c7e49000 r-xp 00000000 08:21
60425741 /usr/lib/libstdc++.so.6.0.13
7f88c7e49000-7f88c8049000 ---p 000f6000 08:21
60425741 /usr/lib/libstdc++.so.6.0.13
7f88c8049000-7f88c8050000 r--p 000f6000 08:21
60425741 /usr/lib/libstdc++.so.6.0.13
7f88c8050000-7f88c8052000 rw-p 000fd000 08:21
60425741 /usr/lib/libstdc++.so.6.0.13
7f88c8052000-7f88c8067000 rw-p 00000000 00:00 0
7f88c8067000-7f88c807d000 r-xp 00000000 08:21
786668 /lib/libz.so.1.2.3.3
7f88c807d000-7f88c827c000 ---p 00016000 08:21
786668 /lib/libz.so.1.2.3.3
7f88c827c000-7f88c827d000 r--p 00015000 08:21
786668 /lib/libz.so.1.2.3.3
7f88c827d000-7f88c827e000 rw-p 00016000 08:21
786668 /lib/libz.so.1.2.3.3
7f88c827e000-7f88c829e000 r-xp 00000000 08:21
786505 /lib/ld-2.11.1.so
7f88c847d000-7f88c8481000 rw-p 00000000 00:00 0
7f88c8499000-7f88c849a000 rw-p 00000000 00:00 0
7f88c849b000-7f88c849d000 rw-p 00000000 00:00 0
7f88c849d000-7f88c849e000 r--p 0001f000 08:21
786505 /lib/ld-2.11.1.so
7f88c849e000-7f88c849f000 rw-p 00020000 08:21
786505 /lib/ld-2.11.1.so
7f88c849f000-7f88c84a0000 rw-p 00000000 00:00 0
7fff8d5f2000-7fff8d607000 rw-p 00000000 00:00
0 [stack]
7fff8d7df000-7fff8d7e0000 r-xp 00000000 00:00
0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00
0 [vsyscall]
Aborted

Aaron Quinlan

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Mar 27, 2012, 11:08:57 AM3/27/12
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Hi Jamie,

Sorry for the delayed response. There have been some issues with moderating posts since the release of the newer Google Groups framework. GenomeCoverageBed no longer requires the use of a genome file (-g) when using BAM as input (as the necessary chomosome size info is already in the BAM header).

Could you try remove the -g option?

Best,
Aaron

Jamie Walters

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Mar 29, 2012, 1:38:57 AM3/29/12
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Aaron

I've tried again without the -g and still get a similar error.
However, all the errors are produced by a pipeline that starts with
Stampy alignments and then goes through dedupping & indel realignment
(GATK). This time I also called GCB on bam files that were from RNA
seq (both RSEM & Tophat). Neither of those gave errors.

Earlier today I also discovered I was getting an error with GATK
Unified genotyper about mis-formed reads ending in a deletion. So now
I suspect perhaps Stampy is producing some sort of formatting errors
that are causing such issues..?? I will try realigning a subset of
reads with different tools to see if I can confirm this.

Jamie

Aaron Quinlan

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Jun 13, 2012, 10:44:51 AM6/13/12
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Hi,
I think this will require inspection of the file.  Could you send me (privately) the smallest file possible that produces the error?

Best,
Aaron

On Jun 10, 2012, at 12:57 AM, farhat...@gmail.com wrote:

I am getting a similar error with genomeCoverageBed. It runs fine for a while then crashes with the below message. It was calculating the coverage of a sorted bam file produced using bwasw.


--------
** glibc detected *** /home/farhat/tmp/software/BEDTools-Version-2.16.2/bin/bedtools: double free or corruption (out): 0x0000000001512a40 ***
======= Backtrace: =========
/lib/libc.so.6(+0x775b6)[0x7f3ad0c7b5b6]
/lib/libc.so.6(cfree+0x73)[0x7f3ad0c81e83]
/home/farhat/tmp/software/BEDTools-Version-2.16.2/bin/bedtools[0x45dfe3]
/home/farhat/tmp/software/BEDTools-Version-2.16.2/bin/bedtools[0x45e60c]
/home/farhat/tmp/software/BEDTools-Version-2.16.2/bin/bedtools[0x45f603]
/home/farhat/tmp/software/BEDTools-Version-2.16.2/bin/bedtools[0x461aed]
/home/farhat/tmp/software/BEDTools-Version-2.16.2/bin/bedtools[0x4368ab]
/lib/libc.so.6(__libc_start_main+0xfd)[0x7f3ad0c22c4d]
/home/farhat/tmp/software/BEDTools-Version-2.16.2/bin/bedtools[0x406d89]
======= Memory map: ========
00400000-00546000 r-xp 00000000 08:61 196108897                          /mnt/disk1/home/farhat/tmp/software/BEDTools-Version-2.16.2/bin/bedtools
00746000-00748000 r--p 00146000 08:61 196108897                          /mnt/disk1/home/farhat/tmp/software/BEDTools-Version-2.16.2/bin/bedtools
.
.
.

Aaron Quinlan

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May 1, 2013, 9:31:56 AM5/1/13
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This looks like you have exceeded the memory available on your machine.  How much memory is available on the box on which genomeCoverageBed is running?


On Apr 30, 2013, at 2:20 PM, John G <johng...@gmail.com> wrote:

I haven't been able to find much info about resolution to this issue and was wondering if there were any updates.  I am running the most recent version of bedtools.  I have about 40 bams that are the product of an alignment to the same reference for all sequences.  When I run genomeCoverageBed, it works fine for the majority of bams.  However, for a handful, it reproducibly fails with the following error:

*** glibc detected *** genomeCoverageBed: double free or corruption (out): 0x00000000018d70e0 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7f7473078b96]
genomeCoverageBed[0x408473]
genomeCoverageBed[0x409e2c]
genomeCoverageBed[0x40afdc]
genomeCoverageBed[0x405c1d]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7f747301b76d]
genomeCoverageBed[0x4049d9]
======= Memory map: ========
00400000-0044b000 r-xp 00000000 103:02 1581643                           /usr/local/src/arq5x-bedtools-322729c/bin/genomeCoverageBed
0064b000-0064c000 r--p 0004b000 103:02 1581643                           /usr/local/src/arq5x-bedtools-322729c/bin/genomeCoverageBed
0064c000-0064d000 rw-p 0004c000 103:02 1581643                           /usr/local/src/arq5x-bedtools-322729c/bin/genomeCoverageBed
01575000-027da000 rw-p 00000000 00:00 0                                  [heap]
7f7472dce000-7f7472f00000 rw-p 00000000 00:00 0
7f7472ffa000-7f74731af000 r-xp 00000000 103:02 3670125                   /lib/x86_64-linux-gnu/libc-2.15.so
7f74731af000-7f74733ae000 ---p 001b5000 103:02 3670125                   /lib/x86_64-linux-gnu/libc-2.15.so
7f74733ae000-7f74733b2000 r--p 001b4000 103:02 3670125                   /lib/x86_64-linux-gnu/libc-2.15.so
7f74733b2000-7f74733b4000 rw-p 001b8000 103:02 3670125                   /lib/x86_64-linux-gnu/libc-2.15.so
7f74733b4000-7f74733b9000 rw-p 00000000 00:00 0
7f74733b9000-7f74733ce000 r-xp 00000000 103:02 3673824                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7f74733ce000-7f74735cd000 ---p 00015000 103:02 3673824                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7f74735cd000-7f74735ce000 r--p 00014000 103:02 3673824                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7f74735ce000-7f74735cf000 rw-p 00015000 103:02 3673824                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7f74735cf000-7f74736ca000 r-xp 00000000 103:02 3670133                   /lib/x86_64-linux-gnu/libm-2.15.so
7f74736ca000-7f74738c9000 ---p 000fb000 103:02 3670133                   /lib/x86_64-linux-gnu/libm-2.15.so
7f74738c9000-7f74738ca000 r--p 000fa000 103:02 3670133                   /lib/x86_64-linux-gnu/libm-2.15.so
7f74738ca000-7f74738cb000 rw-p 000fb000 103:02 3670133                   /lib/x86_64-linux-gnu/libm-2.15.so
7f74738cb000-7f74739ad000 r-xp 00000000 103:02 794168                    /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7f74739ad000-7f7473bac000 ---p 000e2000 103:02 794168                    /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7f7473bac000-7f7473bb4000 r--p 000e1000 103:02 794168                    /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7f7473bb4000-7f7473bb6000 rw-p 000e9000 103:02 794168                    /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7f7473bb6000-7f7473bcb000 rw-p 00000000 00:00 0
7f7473bcb000-7f7473be1000 r-xp 00000000 103:02 3673877                   /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7f7473be1000-7f7473de0000 ---p 00016000 103:02 3673877                   /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7f7473de0000-7f7473de1000 r--p 00015000 103:02 3673877                   /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7f7473de1000-7f7473de2000 rw-p 00016000 103:02 3673877                   /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7f7473de2000-7f7473e04000 r-xp 00000000 103:02 3670139                   /lib/x86_64-linux-gnu/ld-2.15.so
7f7473eeb000-7f7473ff0000 rw-p 00000000 00:00 0
7f7474002000-7f7474004000 rw-p 00000000 00:00 0
7f7474004000-7f7474005000 r--p 00022000 103:02 3670139                   /lib/x86_64-linux-gnu/ld-2.15.so
7f7474005000-7f7474007000 rw-p 00023000 103:02 3670139                   /lib/x86_64-linux-gnu/ld-2.15.so
7fffb62cc000-7fffb62ed000 rw-p 00000000 00:00 0                          [stack]
7fffb6377000-7fffb6378000 r-xp 00000000 00:00 0                          [vdso]

ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
Aborted (core dumped)
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John

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May 1, 2013, 9:45:45 AM5/1/13
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I ran it on a 150 gb machine as well as a 1tb machine.  I am fairly confident it is not lack of memory, but it does seem like a strange error.  These are bacterial plasmid alignments, not very high copy, so it does not consume much. I will look at exact usage in the log file when I am logged on to verify this.

FYI, I also get the same error with a previous version.

Any other thoughts as to things I could check?

Thanks,
John
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Aaron Quinlan

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May 1, 2013, 9:47:38 AM5/1/13
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Would it be possible to share (privately) one of the offending BAMs so that I can diagnose this?

John

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May 1, 2013, 9:50:15 AM5/1/13
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Sure.  I will send it along once I get to the office.  Thanks for taking a look!  It will probably come from my work email, which is jgil...@tgen.org.

John

roye....@gmail.com

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Dec 18, 2014, 10:50:41 AM12/18/14
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Aaron, was this issue eventually resolved?  I seem to have gotten something similar, and oddly it was also with alignment to bacterial plasmids:

On an Ubuntu server with 128 GB RAM, 

samtools view -b <my.bam> | bedtools2-2.20.1/bin/bedtools genomecov -d -ibam stdin | awk '$3!=0' > <covered_bases.txt>

*** glibc detected *** bedtools2-2.20.1/bin/bedtools: double free or corruption (out): 0x0000000007c12460 ***

======= Backtrace: =========

/lib/x86_64-linux-gnu/libc.so.6(+0x7e626)[0x7f81e4e40626]

bedtools2-2.20.1/bin/bedtools[0x48f907]

bedtools2-2.20.1/bin/bedtools[0x48fddd]

bedtools2-2.20.1/bin/bedtools[0x49116a]

bedtools2-2.20.1/bin/bedtools[0x4942b9]

bedtools2-2.20.1/bin/bedtools[0x4082a5]

/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7f81e4de376d]

bedtools2-2.20.1/bin/bedtools[0x40cf79]

======= Memory map: ========

00400000-005b0000 r-xp 00000000 00:21 33115680                           /specific/a/nas-eran-01/groups/eran_halperin/rozovr/bedtools2-2.20.1/bin/bedtools

007b0000-007b4000 r--p 001b0000 00:21 33115680                           /specific/a/nas-eran-01/groups/eran_halperin/rozovr/bedtools2-2.20.1/bin/bedtools

007b4000-007b5000 rw-p 001b4000 00:21 33115680                           /specific/a/nas-eran-01/groups/eran_halperin/rozovr/bedtools2-2.20.1/bin/bedtools

007b5000-07cdc000 rw-p 00000000 00:00 0                                  [heap]

7f81df36c000-7f81e0b6d000 rw-p 00000000 00:00 0 

7f81e4dc2000-7f81e4f75000 r-xp 00000000 00:0e 42655649                   /lib/x86_64-linux-gnu/libc-2.15.so

7f81e4f75000-7f81e5174000 ---p 001b3000 00:0e 42655649                   /lib/x86_64-linux-gnu/libc-2.15.so

7f81e5174000-7f81e5178000 r--p 001b2000 00:0e 42655649                   /lib/x86_64-linux-gnu/libc-2.15.so

7f81e5178000-7f81e517a000 rw-p 001b6000 00:0e 42655649                   /lib/x86_64-linux-gnu/libc-2.15.so

7f81e517a000-7f81e517f000 rw-p 00000000 00:00 0 

7f81e517f000-7f81e5194000 r-xp 00000000 00:16 32499184                   /usr/local/stow/gcc-4.8.0/lib/gcc-4.8.0/lib64/libgcc_s.so.1

7f81e5194000-7f81e5394000 ---p 00015000 00:16 32499184                   /usr/local/stow/gcc-4.8.0/lib/gcc-4.8.0/lib64/libgcc_s.so.1

7f81e5394000-7f81e5395000 rw-p 00015000 00:16 32499184                   /usr/local/stow/gcc-4.8.0/lib/gcc-4.8.0/lib64/libgcc_s.so.1

7f81e5395000-7f81e548e000 r-xp 00000000 00:0e 42655648                   /lib/x86_64-linux-gnu/libm-2.15.so

7f81e548e000-7f81e568d000 ---p 000f9000 00:0e 42655648                   /lib/x86_64-linux-gnu/libm-2.15.so

7f81e568d000-7f81e568e000 r--p 000f8000 00:0e 42655648                   /lib/x86_64-linux-gnu/libm-2.15.so

7f81e568e000-7f81e568f000 rw-p 000f9000 00:0e 42655648                   /lib/x86_64-linux-gnu/libm-2.15.so

7f81e568f000-7f81e5773000 r-xp 00000000 00:16 10043044                   /usr/local/stow/gcc-4.8.0/lib/gcc-4.8.0/lib64/libstdc++.so.6.0.18

7f81e5773000-7f81e5973000 ---p 000e4000 00:16 10043044                   /usr/local/stow/gcc-4.8.0/lib/gcc-4.8.0/lib64/libstdc++.so.6.0.18

7f81e5973000-7f81e597b000 r--p 000e4000 00:16 10043044                   /usr/local/stow/gcc-4.8.0/lib/gcc-4.8.0/lib64/libstdc++.so.6.0.18

7f81e597b000-7f81e597d000 rw-p 000ec000 00:16 10043044                   /usr/local/stow/gcc-4.8.0/lib/gcc-4.8.0/lib64/libstdc++.so.6.0.18

7f81e597d000-7f81e5992000 rw-p 00000000 00:00 0 

7f81e5992000-7f81e59a8000 r-xp 00000000 00:0e 34628217                   /lib/x86_64-linux-gnu/libz.so.1.2.3.4

7f81e59a8000-7f81e5ba7000 ---p 00016000 00:0e 34628217                   /lib/x86_64-linux-gnu/libz.so.1.2.3.4

7f81e5ba7000-7f81e5ba8000 r--p 00015000 00:0e 34628217                   /lib/x86_64-linux-gnu/libz.so.1.2.3.4

7f81e5ba8000-7f81e5ba9000 rw-p 00016000 00:0e 34628217                   /lib/x86_64-linux-gnu/libz.so.1.2.3.4

7f81e5ba9000-7f81e5bcb000 r-xp 00000000 00:0e 42655651                   /lib/x86_64-linux-gnu/ld-2.15.so

7f81e5d79000-7f81e5d7f000 rw-p 00000000 00:00 0 

7f81e5dc6000-7f81e5dcb000 rw-p 00000000 00:00 0 

7f81e5dcb000-7f81e5dcc000 r--p 00022000 00:0e 42655651                   /lib/x86_64-linux-gnu/ld-2.15.so

7f81e5dcc000-7f81e5dce000 rw-p 00023000 00:0e 42655651                   /lib/x86_64-linux-gnu/ld-2.15.so

7fff51876000-7fff51897000 rw-p 00000000 00:00 0                          [stack]

7fff519b1000-7fff519b2000 r-xp 00000000 00:00 0                          [vdso]

ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]

Abort 


Aaron Quinlan

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Dec 18, 2014, 1:00:02 PM12/18/14
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To be completely honest, I can’t remember if this was ever resolved and I don’t have an email record beyond what is on Google Groups.

- Aaron





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John Gillece

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Dec 18, 2014, 2:02:14 PM12/18/14
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As far as I know, it was not resolved as I didn't hear back.


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roye rozov

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Dec 18, 2014, 2:02:14 PM12/18/14
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Alright, in spite of the crash it looks like enough of the file was processed for my needs.  Thanks for following up.


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