Error with floating point exception about methyldackel HOT 9 CLOSED

Can you try the most recent version (0.1.12)? I suspect this is related to #23, which is fixed in that release.

from methyldackel.

If that doesn't fix it, can you provide me with the BAM file? I can debug this and release a fixed version then.

from methyldackel.

Hi,
I am using the recent version
./PileOMeth --version
0.1.12-dirty (using HTSlib version 1.2.1)

Yes sure! Here is the bam file
https://drive.google.com/file/d/0B9AIw0gsTy_zNkxuUWk4aVlndW8/view?usp=sharing

Thanks!

from methyldackel.

I can't seem to reproduce this locally with 0.1.12. Can you recompile with make install OPTS="-g -O0" ... and then rerun it in gdb (gdb --args PileOMeth extract --CHG --CHH ~/whole_genome_TAIR10/TAIR10_all.fa 32338_CTTGTA_C89J6ANXX_3_20160105B_20160105_2.modified.bam)? Presumably that'll produce the same exception and you can then type bt to get a backtrace.

from methyldackel.

Recompiling didnt solve the issue!
Here is the error with gdb
gdb -args ~/Softwares/PileOMeth/newCompile/PileOMeth extract --CHG --CHH ~/whole_genome_TAIR10/TAIR10_all.fa 36841_GCCAAT_C92VAANXX_1_20160229B_20160229.modified.bam
GNU gdb (GDB) 7.5.1
Copyright (C) 2012 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-unknown-linux-gnu".
For bug reporting instructions, please see:
http://www.gnu.org/software/gdb/bugs/...
Reading symbols from /home/GMI/rahul.pisupati/Softwares/PileOMeth/newCompile/PileOMeth...done.
(gdb) run
Starting program: ~/Softwares/PileOMeth/newCompile/PileOMeth extract --CHG --CHH /home/GMI/rahul.pisupati/whole_genome_TAIR10/TAIR10_all.fa 36841_GCCAAT_C92VAANXX_1_20160229B_20160229.modified.bam
warning: no loadable sections found in added symbol-file system-supplied DSO at 0x2aaaaaacb000
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]
Using host libthread_db library "/lib64/libthread_db.so.1".
writing to prefix:'36841_GCCAAT_C92VAANXX_1_20160229B_20160229.modified'

Program received signal SIGFPE, Arithmetic exception.
0x000000000040fc0a in faidx_fetch_seq (fai=0x4702a0, c_name=0x4f2390 "Chr1", p_beg_i=-1, p_end_i=-1, len=0x7fffffff2b5c) at faidx.c:455
455 int ret = bgzf_useek(fai->bgzf, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % val.line_blen, SEEK_SET);
(gdb) bt
#0 0x000000000040fc0a in faidx_fetch_seq (fai=0x4702a0, c_name=0x4f2390 "Chr1", p_beg_i=-1, p_end_i=-1, len=0x7fffffff2b5c) at faidx.c:455
#1 0x0000000000404872 in extractCalls (config=0x7fffffff2c60) at extract.c:155
#2 0x0000000000405a51 in extract_main (argc=, argv=) at extract.c:627
#3 0x0000000000403103 in main (argc=6, argv=0x7fffffff2e38) at main.c:37
(gdb) next

Program terminated with signal SIGFPE, Arithmetic exception.
The program no longer exists.

from methyldackel.

This appears to be an issue with the fasta file. Can you post that somewhere?

from methyldackel.

This is the TAIR10 arabidopsis genome file. Anyway I have uploaded it in here
https://drive.google.com/file/d/0B9AIw0gsTy_zTW9oVS1SZjg4S0U/view?usp=sharing

from methyldackel.

I think I figured this out. I chop the header to just the chromosome name (removing the rest) and indexing it again. It gave me no error. I dont know why that is the case.

Thank you!!
Rahul

from methyldackel.

Weird stuff, don't know why that caused an issue either but glad it's working now :)

from methyldackel.