bamcat syscall error

[guillermo-carrasco]

Hi,

When executing bamcat command I get the following message:

 login01 /scratch/gcarrasco/tests/test_bcbio_cwl ~> bamcat
libmaus2::util::PosixExecute::execute() donotthrow: "addr2line --exe=bamcat 0x4140a0" exited with status 1
libmaus2::util::PosixExecute::execute() donotthrow: failing command was addr2line --exe=bamcat 0x4140a0
libmaus2::util::PosixExecute::execute() donotthrow: failed syscall  login01

Besides that, the program seems to work. We're running Linux Centos 6.6 in our cluster and the package was installed via conda.

Any clue of why this may be happening?

Thanks a lot in advance,

[gt1]

Hi,

error messages from biobambam2 are reported including a stack trace to show where they originate from. To make the stack trace more useful it tries to convert the addresses to function names using the addr2line program. This program seems to be missing on your system. The message can be safely ignored. The error produced by just calling bamcat without any arguments and stream redirections is that it refuses to produce a (binary) BAM file in a terminal.

Best, German

[guillermo-carrasco]

Hi German,

Thank you for your answer.

Both programs bamcat and addr2line seem to be correctly installed:

 login01 /scratch/gcarrasco/tests ~> which bamcat
/cm/shared/apps/bcbio/20150720-devel/tools/bin/bamcat

 login01 /scratch/gcarrasco/tests ~> which addr2line
/usr/bin/addr2line

However, trying to execute the addr2line command alone, I get this:

login01 /scratch/gcarrasco/tests ~> addr2line --exe=bamcat 0c4140a0
addr2line: 'bamcat': No such file

Adding the full path, I get what it seems to be a "correct" answer (not very readable though):

login01 /scratch/gcarrasco/tests ~> addr2line --exe=`which bamcat` 0c4140a0
??:0

Could that be the problem?

Thanks again

[gt1]

Hi,

yes, that would explain it. I have disabled calling addr2line for non debug builds of libmaus2/biobambam2 and also implemented detection of the full binary path, so this error should disappear.

Best, German

[guillermo-carrasco]

Thanks so much German!