bamsort crash at libmaus2::lz::BgzfDeflateParallel::flush about biobambam2

[mmokrejs]

A single-threaded run does not dump a core file, the stacktrace seems same on two attempts at least but I cannot convert it into a meaningful output.

bamsort SO=queryname inputthreads=10 outputthreads=1 level=9 index=1 O=HFYJ5AFXX.5kb.fragments-6.namesorted.bam I=HFYJ5AFXX.5kb.fragments-6.refsorted.bam
[V] Reading alignments from source.
[V] 1M
[V] 2M
[V] 3M
[V] 4M
[V] 5M
[V] 6M
[V] 7M
[V] 8M
[V] 9M
[V] 10M
[V] 11M
[V] 12M
[V] 13M
[V] 14M
[V] 15M
[V] 16M
[V] 17M
[V] 18M
[V] read 19175378 alignments
[V] producing sorted output
File is not sorted by coordinate.

/apps/gentoo/usr/lib64/libmaus2.so.2(libmaus2::util::StackTrace::StackTrace()+0x68)[0x2aaaab59ef30]
bamsort(libmaus2::exception::LibMausException::LibMausException()+0x2b)[0x2aaaaab22dcb]
bamsort(+0xc37c5)[0x2aaaaab6e7c5]
bamsort(+0xc43e6)[0x2aaaaab6f3e6]
bamsort(+0x139336)[0x2aaaaabe4336]
bamsort(+0xff60b)[0x2aaaaabaa60b]
bamsort(+0xd2428)[0x2aaaaab7d428]
bamsort(+0xd2395)[0x2aaaaab7d395]
bamsort(+0x1c820d)[0x2aaaaac7320d]
bamsort(+0x1c7c4b)[0x2aaaaac72c4b]
bamsort(+0x155b14)[0x2aaaaac00b14]
bamsort(+0x129af6)[0x2aaaaabd4af6]
bamsort(+0xe9c41)[0x2aaaaab94c41]
bamsort(+0x7245e)[0x2aaaaab1d45e]
bamsort(+0x754fa)[0x2aaaaab204fa]
/apps/gentoo/lib64/libc.so.6(__libc_start_main+0xea)[0x2aaaad08c4fa]
bamsort(+0x6c96a)[0x2aaaaab1796a]

The input file was freshly sorted by coordinates and bamsort did not crash. So, I consider the message File is not sorted by coordinate. bogus. Please improve the error message to say what is the input file and what record it complains about.

I have debug symbols for the libs and binaries but they are split aside from the executables and lib files into a separate directory. This is thanks to FEATURES="splitdebug nostrip" of my Gentoo Linux.

See https://wiki.gentoo.org/wiki/Project:Quality_Assurance/Backtraces .

[mmokrejs]

I gave it another short from within gdb but I probably need to set a breakpoint somehow in advance? Where to?

$ gdb -q /apps/gentoo/usr/bin/bamsort
...
(gdb) set args SO=queryname inputthreads=10 outputthreads=1 level=9 index=1 O=HFYJ5AFXX.5kb.fragments-6.namesorted.bam I=HFYJ5AFXX.5kb.fragments-6.refsorted.bam
(gdb) run
Starting program: /apps/gentoo/usr/bin/bamsort SO=queryname inputthreads=10 outputthreads=1 level=9 index=1 O=HFYJ5AFXX.5kb.fragments-6.namesorted.bam I=HFYJ5AFXX.5kb.fragments-6.refsorted.bam
warning: Could not load shared library symbols for linux-vdso.so.1.
Do you need "set solib-search-path" or "set sysroot"?
[Thread debugging using libthread_db enabled]
[New Thread 0x2aaaaef4f700 (LWP 104102)]
[New Thread 0x2aaaaf150700 (LWP 104103)]
[New Thread 0x2aaab8200700 (LWP 104104)]
[New Thread 0x2aaab8401700 (LWP 104105)]
[New Thread 0x2aaac4200700 (LWP 104106)]
[New Thread 0x2aaac4401700 (LWP 104107)]
[New Thread 0x2aaad0200700 (LWP 104108)]
[New Thread 0x2aaad0401700 (LWP 104109)]
[New Thread 0x2aaadc200700 (LWP 104110)]
[New Thread 0x2aaadc401700 (LWP 104111)]
[V] Reading alignments from source.
[V] 1M
[V] 2M
[V] 3M
[V] 4M
[V] 5M
[V] 6M
[V] 7M
[V] 8M
[V] 9M
[V] 10M
[V] 11M
[V] 12M
[V] 13M
[V] 14M
[V] 15M
[V] 16M
[V] 17M
[V] 18M
[V] read 19175378 alignments
[V] producing sorted output
[Thread 0x2aaac4200700 (LWP 104106) exited]
[Thread 0x2aaadc200700 (LWP 104110) exited]
[Thread 0x2aaab8200700 (LWP 104104) exited]
[Thread 0x2aaadc401700 (LWP 104111) exited]
[Thread 0x2aaad0401700 (LWP 104109) exited]
[Thread 0x2aaad0200700 (LWP 104108) exited]
[Thread 0x2aaac4401700 (LWP 104107) exited]
[Thread 0x2aaaaf150700 (LWP 104103) exited]
[Thread 0x2aaab8401700 (LWP 104105) exited]
[Thread 0x2aaaaef4f700 (LWP 104102) exited]
File is not sorted by coordinate.

/apps/gentoo/usr/lib64/libmaus2.so.2(libmaus2::util::StackTrace::StackTrace()+0x68)[0x2aaaab59ef30]
/apps/gentoo/usr/bin/bamsort(libmaus2::exception::LibMausException::LibMausException()+0x2b)[0x2aaaaab22dcb]
/apps/gentoo/usr/bin/bamsort(+0xc37c5)[0x2aaaaab6e7c5]
/apps/gentoo/usr/bin/bamsort(+0xc43e6)[0x2aaaaab6f3e6]
/apps/gentoo/usr/bin/bamsort(+0x139336)[0x2aaaaabe4336]
/apps/gentoo/usr/bin/bamsort(+0xff60b)[0x2aaaaabaa60b]
/apps/gentoo/usr/bin/bamsort(+0xd2428)[0x2aaaaab7d428]
/apps/gentoo/usr/bin/bamsort(+0xd2395)[0x2aaaaab7d395]
/apps/gentoo/usr/bin/bamsort(+0x1c820d)[0x2aaaaac7320d]
/apps/gentoo/usr/bin/bamsort(+0x1c7c4b)[0x2aaaaac72c4b]
/apps/gentoo/usr/bin/bamsort(+0x155b14)[0x2aaaaac00b14]
/apps/gentoo/usr/bin/bamsort(+0x129af6)[0x2aaaaabd4af6]
/apps/gentoo/usr/bin/bamsort(+0xe9c41)[0x2aaaaab94c41]
/apps/gentoo/usr/bin/bamsort(+0x7245e)[0x2aaaaab1d45e]
/apps/gentoo/usr/bin/bamsort(+0x754fa)[0x2aaaaab204fa]
/apps/gentoo/lib64/libc.so.6(__libc_start_main+0xea)[0x2aaaad08c4fa]
/apps/gentoo/usr/bin/bamsort(+0x6c96a)[0x2aaaaab1796a]


Program exited with code 01.
(gdb) where
No stack.
(gdb) bt
No stack.
(gdb) 

[gt1]

Hi,

I am happy to look into it, but the problem is that you are asking for a BAM index (BAI/CSI) on an output file which is sorted in query name order (esp. not coordinate order). BAM indexing requires coordinate order, so this will never work. Arguable the program could check this upfront and provide a more human readable error message. Anyway, the problem should not crash while reporting the error, and this needs to be fixed. Thanks for the report.

Best,
German

[mmokrejs]

Hi German,
ah you are right, I forgot about this. I had the same question myself "how come that bamsort allows me index=1 while samtools sort dies if I ask it to index a queryname-sorted file?". I forgot.

But please make bamsort silently ignore the index=1 argument, it is more helpful if one loops over many files. Thank you.