buffer overflow error
Closed this issue · 4 comments
Running rascaf directly from a clone of the master branch and downloading the v.1.0.0 source resulting in the following error:
Found 147832 exon blocks.
Found 113960 gene blocks.
Found 2281 non-trivial gene block components.
*** buffer overflow detected ***: /home/peter/bioinformatics/Rascaf-1.0.0/rascaf terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x7338f)[0x7fbdc6b7a38f]
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7fbdc6c11c9c]
/lib/x86_64-linux-gnu/libc.so.6(+0x109b60)[0x7fbdc6c10b60]
/lib/x86_64-linux-gnu/libc.so.6(+0x10a0f4)[0x7fbdc6c110f4]
/home/peter/bioinformatics/Rascaf-1.0.0/rascaf[0x403ae5]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7fbdc6b28ec5]
/home/peter/bioinformatics/Rascaf-1.0.0/rascaf[0x403f7f]
etc.
Running make didn't suggest any compilation errors. The OS is Ubuntu 14.04. Is there are a sample dataset that might be used to test the installation?
Can you please show me the command line you use? Can you see anything output to the result file specified from -o option (default output file is rascaf.out).
I'll create and upload a sample data set later.
Thanks.
The command I'm using is the same as in the sample,
rascaf -b A.bam -f assembly.fa -o A
The A.out file begins as follows:
Contigs
0: scaffold10000_size206 1 206
1: scaffold10001_size206 1 206
2: scaffold10002_size206 1 206
3: scaffold10003_size206 1 206
4: scaffold10004_size206 1 206
5: scaffold10005_size206 1 206
6: scaffold10006_size206 1 206
7: scaffold10007_size206 1 206
8: scaffold10008_size206 1 206
9: scaffold10009_size206 1 206
10: scaffold1000_size26079 1 124
...
And continues until the end which is:
116307 scaffold_j128_1 99476 (18240 19653): (116308 scaffold_j128_1 99477 (19704 21040)):(1 2)
116308 scaffold_j128_1 99477 (19704 21040): (116307 scaffold_j128_1 99476 (18240 19653)):(2 2)
116309 scaffold_j128_1 99477 (21097 21124):
116310 scaffold_j128_1 99477 (21205 22036):
116311 scaffold_j128_1 99477 (22342 22499):
116312 scaffold_j128_1 99477 (22635 26001):
command line: /home/peter/bioinformatics/Rascaf/rascaf -b
It seems the error happens when it trying to resolve the path to the alignment file. I've uploaded a more robust version. Can you give it a try?
From the output, are you also using the verbose mode?
Thanks
The new version completed without error! The previous error was generated with the verbose mode flag included. Thanks for your help.