Comments (8)
OgraphBin is still in dev and should not be yet used.
from bcalm.
so we should use graph3?
from bcalm.
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)
from bcalm.
I'll take care of it.
Thanks for the example
from bcalm.
okay thanks!
from bcalm.
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.
from bcalm.
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.
from bcalm.
it was related to a call in initBinSeq, that I just commented out because we don't use binSeq at the moment.
from bcalm.
Related Issues (20)
- Output of bcalm2 similar to minia 3.2.1 unitigs? HOT 2
- Memory error with many reference genomes as input HOT 16
- High frequency of nodes with degree of two with length = 2k-1 HOT 2
- .fa files contain lowercase `km` instead of the documented uppercase `KM` HOT 3
- bcalm 2.2.1 on conda for Mac OS X produces incorrect cDBG (the zombie bug returns!!) HOT 12
- Add better input parsing HOT 1
- Improve error message for bad fasta input HOT 1
- Apparently bcalm crashes with very large k's (4096) HOT 1
- bcalm -version return code 1 to shell
- Glue is too strong, because glue files are not deleted.
- insert unitig disregarding the reverse complement HOT 1
- Option `-out-dir` is not used ? HOT 1
- bug report on a metagenomics dataset HOT 3
- Add header description with `-all-abundance-counts` HOT 2
- Is the output file reproducible? HOT 2
- Set the minimum value of -kmer-size HOT 1
- Counting kmers error HOT 2
- Fails to build from source on ARM MacOS HOT 1
- When multiple inputs specified, BCALM silently loses data
- No version printed when installed with Bioconda and executed with the `-version` flag
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from bcalm.