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Comments (8)

Malfoy avatar Malfoy commented on August 25, 2024

OgraphBin is still in dev and should not be yet used.

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rchikhi avatar rchikhi commented on August 25, 2024

so we should use graph3?

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rchikhi avatar rchikhi commented on August 25, 2024

ograph3 has an issue as well:

[..]
[Iterating DSK partitions                ]  75   %   elapsed:   3 min 17 sec   remaining:   1 min 6  sec
Partition 25 has 1520 kmers
Loaded 503 doubled kmers for partition 25
Iterated 1520 kmers, among them 403 has leftmin!=rightmin
==7688== Conditional jump or move depends on uninitialised value(s)
==7688==    at 0xF8C928: graph3::debruijn() (ograph.cpp:362)
==7688==    by 0xF95771: bcalm_1::execute()::{lambda(int)#6}::operator()(int) const (bcalm_1.cpp:485)
[..]

To reproduce it:

../build/bcalm -in ~/bcalm-data/lambda-k16.fa -k 16 -abundance 1

https://transfer.sh/9h7XC/lambda-k16.fa (link will expire soon)

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Malfoy avatar Malfoy commented on August 25, 2024

I'll take care of it.
Thanks for the example

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rchikhi avatar rchikhi commented on August 25, 2024

okay thanks!

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Malfoy avatar Malfoy commented on August 25, 2024

I can't reproduce the error.
But I see a possible reason for bcalm to crash.
I tried a fix, tell me if it work for you.

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rchikhi avatar rchikhi commented on August 25, 2024

Indeed, with this new version, I do not get a valgrind error during the execution anymore!
This bug was unrelated then, but thanks for fixing it.

The crash remains at the end of the execution, however it disappears when bcalm is compiled in debug mode. Valgrind output is not helpful without debug information.

==9529== Invalid read of size 4
==9529==    at 0x7091E2: __tcf_3 (in /home/rayan/bcalm-gatb/build/bcalm)
==9529==    by 0x5CCAB28: __run_exit_handlers (exit.c:82)
==9529==    by 0x5CCAB74: exit (exit.c:104)
==9529==    by 0x5CB4B4B: (below main) (libc-start.c:321)
==9529==  Address 0x8f0109e1b0 is not stack'd, malloc'd or (recently) free'd

Neither is gdb:

Program received signal SIGSEGV, Segmentation fault.
0x00000000007091e2 in __tcf_3 ()
(gdb) bt
#0  0x00000000007091e2 in __tcf_3 ()
#1  0x00007ffff6c0ab29 in __run_exit_handlers (status=0, listp=0x7ffff6f785a8 <__exit_funcs>, run_list_atexit=run_list_atexit@entry=true) at exit.c:82
#2  0x00007ffff6c0ab75 in __GI_exit (status=<optimized out>) at exit.c:104
#3  0x00007ffff6bf4b4c in __libc_start_main (main=0x6edf50 <main>, argc=7, argv=0x7fffffffdc18, init=<optimized out>, fini=<optimized out>,
    rtld_fini=<optimized out>, stack_end=0x7fffffffdc08) at libc-start.c:321
#4  0x00000000006ee9cf in _start ()

I'm on it.

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rchikhi avatar rchikhi commented on August 25, 2024

it was related to a call in initBinSeq, that I just commented out because we don't use binSeq at the moment.

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