Problems running the bam-readcount program: can NOT get started

Question

[sunyan727]

Hi all,

I want to use bam-readcount pipeline, so I followed the instruction and installed it.

When I tried to use bam-readcount to analyze my bam file, it just can not get started.

Here is what I did:

./bam-readcount/bin/bam-readcount -f hg19.fa -l site_list  case.bam> ./case.rc

The "site_list" file looks like this:

chr1    9995    9995
chr1    10000   10000

And here comes the error:

Minimum mapping quality is set to 0
Expect library: WHRDHUMdneRAEAAAA-66 in BAM
*** glibc detected *** ./bam-readcount/bin/bam-readcount: munmap_chunk(): invalid pointer: 0x00007fffa3fc73d0 ***
======= Backtrace: =========
/lib64/libc.so.6(cfree+0x166)[0x3457c729d6]
./bam-readcount/bin/bam-readcount(main+0x17c5)[0x424fd5]
/lib64/libc.so.6(__libc_start_main+0xf4)[0x3457c1d994]
./bam-readcount/bin/bam-readcount(__gxx_personality_v0+0x1a1)[0x4217b9]
======= Memory map: ========
00400000-00480000 r-xp 00000000 00:31 8993879798                         ./bam-readcount/bin/bam-readcount
0067f000-00680000 rw-p 0007f000 00:31 8993879798                         ./bam-readcount/bin/bam-readcount
00680000-00681000 rw-p 00680000 00:00 0
03393000-042ff000 rw-p 03393000 00:00 0                                  [heap]
3457800000-345781c000 r-xp 00000000 08:01 12946514                       /lib64/ld-2.5.so
3457a1b000-3457a1c000 r--p 0001b000 08:01 12946514                       /lib64/ld-2.5.so
3457a1c000-3457a1d000 rw-p 0001c000 08:01 12946514                       /lib64/ld-2.5.so
3457c00000-3457d4e000 r-xp 00000000 08:01 12946515                       /lib64/libc-2.5.so
3457d4e000-3457f4e000 ---p 0014e000 08:01 12946515                       /lib64/libc-2.5.so
3457f4e000-3457f52000 r--p 0014e000 08:01 12946515                       /lib64/libc-2.5.so
3457f52000-3457f53000 rw-p 00152000 08:01 12946515                       /lib64/libc-2.5.so
3457f53000-3457f58000 rw-p 3457f53000 00:00 0
3458000000-3458082000 r-xp 00000000 08:01 12946516                       /lib64/libm-2.5.so
3458082000-3458281000 ---p 00082000 08:01 12946516                       /lib64/libm-2.5.so
3458281000-3458282000 r--p 00081000 08:01 12946516                       /lib64/libm-2.5.so
3458282000-3458283000 rw-p 00082000 08:01 12946516                       /lib64/libm-2.5.so
3458800000-3458816000 r-xp 00000000 08:01 12946523                       /lib64/libpthread-2.5.so
3458816000-3458a15000 ---p 00016000 08:01 12946523                       /lib64/libpthread-2.5.so
3458a15000-3458a16000 r--p 00015000 08:01 12946523                       /lib64/libpthread-2.5.so
3458a16000-3458a17000 rw-p 00016000 08:01 12946523                       /lib64/libpthread-2.5.so
.....
.....
.....

Any idea what might be the problem?

Thanks!

[WouterDeCoster]

I added markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

[sunyan727]

Thank you so much for your help~~

[WouterDeCoster]

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your post but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

[BioinfGuru]

"glibc detected invalid pointer" is the error

The GNU C library (glibc)][1] provides the core libraries for running systems that use the Linux Kernal. The pointer "0x00007fffa3fc73d0" is invalid. This is telling you that address "0x00007fffa3fc73d0" is not storing what it should be storing

My guess is either:

1) the infile contains a line that the program can't handle...are you sure every line looks like this "chr1 9995 9995" - are there any lines with unsusual chromosome names? Create a test file with 10 lines where the first column only contains "chr1" - does that fix the problem?

2) something has gone wrong with installation of the program

3) the command has a synthax error

4) the gods just dont like you

With an error like this - to do with computer memory - I think youd probably get better gudance on stack overflow