segmentation fault (core dumped)

[GoogleCodeExporter]

Hello,

I am using JointSNVMix for the first time. I've completed the installation and 
I wanted to try a run, with the minimum of parameters.
I am using the version 0.8-b2.

I launched the software this way:
[root@U1009-PCJane JointSNVMix-0.8-b2]# jsm.py classify /home/merlevede/hg19.fa 
/data/patient1/s_garma-fibros_converted_sorted.bam 
/data/patient1/s_garma-296_converted_sorted.bam 
chrom   position    ref_base    var_base    normal_counts_a normal_counts_b tumour_counts_a
    tumour_counts_b p_AA_AA p_AA_AB p_AA_BB p_AB_AA p_AB_ABp_AB_BB  p_BB_AA p_BB_AB 
p_BB_BB
Erreur de segmentation (core dumped)

I tried also with the version 0.8-b1 and I have the same problem.
Do you know what could be the reason for this segmentation fault? I haven't 
changed anything in the code...

Thank you for your help,
Jane

Original issue reported on code.google.com by jane.mer...@gmail.com on 27 Feb 2012 at 2:45

[GoogleCodeExporter]

Hi Jane,
Segmentation faults are hard to reproduce, but the following information will 
help.

1) Your operating system.
2) The samtools version used manipulate the files. (Or if you use GATK, Picard 
etc the version of those.
3) The aligner used.
4) Information about any other programs that edited/manipulated FASTQ/BAM files 
to give the input used.

The following will give me some information about the file, but should not 
reveal anything confidential about the data. Use these at your discretion.

4)The output of `samtools view -H BAM_FILE`. For each BAM will give be the 
header which usually just states which chromosomes are present in the BAM.
5) The output of `grep \> FASTAFILE`. This will tell me which chromosomes are 
in the FASTA file.

Original comment by AndrewJL...@gmail.com on 27 Feb 2012 at 4:51

[GoogleCodeExporter]

Hello,

Thank you for your answer. To reply to these points,
1) I'm using Linux (fedora 16) system with 64 bits.
2) samtools-0.1.18
3) the aligner is Elandv2
4) normal sample :
samtools view -H /data/patient1/s_garma-fibros_converted_sorted.bam
@PG ID:illumina_export2sam.pl   VN:2.0.0    CL:/usr/local/bin/illumina_export2sam.pl 
--read1=s_garma-fibros_1_export.txt --read2=s_garma-fibros_2_export.txt
@SQ SN:chr1 LN:249250621
@SQ SN:chr2 LN:243199373
@SQ SN:chr3 LN:198022430
@SQ SN:chr4 LN:191154276
@SQ SN:chr5 LN:180915260
@SQ SN:chr6 LN:171115067
@SQ SN:chr7 LN:159138663
@SQ SN:chr8 LN:146364022
@SQ SN:chr9 LN:141213431
@SQ SN:chr10    LN:135534747
@SQ SN:chr11    LN:135006516
@SQ SN:chr12    LN:133851895
@SQ SN:chr13    LN:115169878
@SQ SN:chr14    LN:107349540
@SQ SN:chr15    LN:102531392
@SQ SN:chr16    LN:90354753
@SQ SN:chr17    LN:81195210
@SQ SN:chr18    LN:78077248
@SQ SN:chr19    LN:59128983
@SQ SN:chr20    LN:63025520
@SQ SN:chr21    LN:48129895
@SQ SN:chr22    LN:51304566
@SQ SN:chrX LN:155270560
@SQ SN:chrY LN:59373566
@SQ SN:chrMt    LN:16571

tumoral sample:
samtools view -H /data/patient1/s_garma-296_converted_sorted.bam
@PG ID:illumina_export2sam.pl   VN:2.0.0    CL:/usr/local/bin/illumina_export2sam.pl 
--read1=s_garma-296_1_export.txt --read2=s_garma-296_2_export.txt
@SQ SN:chr1 LN:249250621
@SQ SN:chr2 LN:243199373
@SQ SN:chr3 LN:198022430
@SQ SN:chr4 LN:191154276
@SQ SN:chr5 LN:180915260
@SQ SN:chr6 LN:171115067
@SQ SN:chr7 LN:159138663
@SQ SN:chr8 LN:146364022
@SQ SN:chr9 LN:141213431
@SQ SN:chr10    LN:135534747
@SQ SN:chr11    LN:135006516
@SQ SN:chr12    LN:133851895
@SQ SN:chr13    LN:115169878
@SQ SN:chr14    LN:107349540
@SQ SN:chr15    LN:102531392
@SQ SN:chr16    LN:90354753
@SQ SN:chr17    LN:81195210
@SQ SN:chr18    LN:78077248
@SQ SN:chr19    LN:59128983
@SQ SN:chr20    LN:63025520
@SQ SN:chr21    LN:48129895
@SQ SN:chr22    LN:51304566
@SQ SN:chrX LN:155270560
@SQ SN:chrY LN:59373566
@SQ SN:chrMt    LN:16571

5) [merlevede@U1009-PCJane ~]$ grep \> hg19.fa
When paying attention to my fasta file, I realized that I provided a wrong 
fasta file.
I changed it and it is running now. I hope the run will be fine!

I would like to know where to ask questions or find explanation about how to 
run the software for the alternative methods. (I would like to try the 
independent Fisher method, but I haven't found documentation for something else 
that train and classify)

Thanks a lot for your help !
Jane

Original comment by jane.mer...@gmail.com on 27 Feb 2012 at 5:54

[GoogleCodeExporter]

Hi Jane,
This is the right place to file bugs/issues. The best place to pose general 
questions and ask for help is the google group 
http://groups.google.com/group/jointsnvmix-user-group.

With regards to the independent fisher method, I have removed that method among 
others from the 0.8 series of JointSNVMix. If you want to use it, you can use 
the version 0.7.5 series which is actually the current stable version.

Cheers,
Andy

Original comment by AndrewJL...@gmail.com on 27 Feb 2012 at 6:05

[GoogleCodeExporter]

Original comment by AndrewJL...@gmail.com on 8 Dec 2012 at 7:53

• Changed state: WontFix