'Floating Point Exception' Error While Running Somaticsniper

Question

[zhangzhoua]

Hi, I installed SomaticSniper in my CentOS6 following the instruction here. https://github.com/genome/somatic-sniper I have both samtools-0.1.6 and 0.1.8 installed. To get the SomaticSniper compiled, I did "export SAMTOOLS_ROOT=/path/to/samtool-0.1.6" And then it was compiled successfully. However, I got the following error while running it.

"Floating point exception(core dumped) $PATH_SNIPER -f $PATH_REF $T_BAM $N_BAM $OUT_SNIPER "

I read previous post. Some say this error is due to the reference of mapping and SomaticSniper are different. But I checked the reference I used. They are the same human_g1K_v37.

Anyone knows how to fix this error? Thanks in advance!

[rahul.kanwar]

I am also seeing the same "Floating point exception" while running v1.0.4. I am running it on a gene panel. I have checked that I have the same reference in the fasta and the bam files. Thanks!

Answer 1

[tgi.tabbott]

I see the error indicated that a core file was dumped. Is that the case, and if so, is it >0bytes in size? If you have a valid core file, then we can try to get stack trace information from it. To do this, assuming you have gdb installed (which should be the case if the "Development Tools" package group is installed), you can run:

gdb --batch -ex bt $PATH_SNIPER /path/to/core

This may print some useful information that can help us find the problem.

If there is no core file, then all hope is not lost. I'd suggest first recompiling sniper in debug mode by altering the "cmake" step of the build instructions to be:

cmake .. -DCMAKE_BUILD_TYPE=debug

This builds a debug version of the executable with optimizations disabled. You can rerun sniper using this new executable in gdb with the following command:

gdb $PATH_SNIPER

At the (gdb) prompt, enter:

run -f $PATH_REF $T_BAM $N_BAM $OUT_SNIPER > $OUTPUT_FILE

where $OUTPUT_FILE is where you want the sniper output to go. If the program crashes, it should print an error and put you back at the (gdb) prompt. You can get a stack trace here by typing:

bt

To exit gdb, you can type quit or press CTRL+D.

[zhangzhoua]

Thanks a lot! I got the following

(gdb) bt

#0  0x0000000000410171 in fai_fetch (fai=0x620370, str=<value optimized out>, len=0x620038) at faidx.c:289
#1  0x00000000004092c8 in glf_somatic (tid=0, pos=10354, n1=1, n2=1, pl1=0x628cd0, pl2=0x626120, 
    data=0x620010, snp_fh=0x625370)
    at /home/zz/software/genome/somatic-sniper/src/lib/sniper/somatic_sniper.c:114
#2  0x00000000004086ee in bam_sspileup_file (fp1=0x630570, fp2=0x623a50, mask=1796, thresh=0, 
    func=0x409211 <glf_somatic>, func_data=0x620010, snp_fh=0x625370)
    at /home/zz/software/genome/somatic-sniper/src/lib/sniper/sniper_pileup.c:258
#3  0x0000000000404341 in main (argc=6, argv=0x7fffffffe118)
    at /home/zz/software/genome/somatic-sniper/src/exe/bam-somaticsniper/main.c:134

I found where the problem is and finaly got the problem fixed!! It was the index of the reference fasta! I downloaded the human_g1k_v37.fasta and human_g1k_v37.fasta.fai from the gatk bundle. However, this .fai file caused the error. I got a new .fai file by running samtools-0.1.6. And then it worked~!

Thank you very much, Tabbott!

[tgi.tabbott]

No problem. I guess that newer versions of samtools may have an incompatible .fai format. That is good to know!

Answer 2

[Chris Miller]

This error generally occurs when sniper tries to look for a chromosome that isn't there, or tries to look off the end of the chromosome (since the lengths may be different between different version of the reference). Are you sure that your fasta contains all the chromsomes and contigs that are referenced in the header of your bam? Sometimes fastas are created that are just 1-22,X,Y and omit the extra contigs

[zhangzhoua]

Thanks Chris.

I double checked the references. They are in different format (fasta vs. bwa reference), but origin from the same g1k_v37 version.

Any other possible problems? Thanks!

I used the human_g1k_v37.fasta from GATK resource bundle for the SomaticSniper.

And I used the same version (g1k_v37) for bwa mapping.

This is the fasta headers

This is the bam headers.

@HD     VN:1.4  GO:none SO:coordinate
@SQ     SN:1    LN:249250621
@SQ     SN:2    LN:243199373
@SQ     SN:3    LN:198022430
@SQ     SN:4    LN:191154276
@SQ     SN:5    LN:180915260
@SQ     SN:6    LN:171115067
@SQ     SN:7    LN:159138663
@SQ     SN:8    LN:146364022
@SQ     SN:9    LN:141213431
@SQ     SN:10   LN:135534747
@SQ     SN:11   LN:135006516
@SQ     SN:12   LN:133851895
@SQ     SN:13   LN:115169878
@SQ     SN:14   LN:107349540
@SQ     SN:15   LN:102531392
@SQ     SN:16   LN:90354753
@SQ     SN:17   LN:81195210
@SQ     SN:18   LN:78077248
@SQ     SN:19   LN:59128983
@SQ     SN:20   LN:63025520
@SQ     SN:21   LN:48129895
@SQ     SN:22   LN:51304566
@SQ     SN:X    LN:155270560
@SQ     SN:Y    LN:59373566
@SQ     SN:MT   LN:16569
@SQ     SN:GL000207.1   LN:4262
@SQ     SN:GL000226.1   LN:15008
@SQ     SN:GL000229.1   LN:19913
@SQ     SN:GL000231.1   LN:27386
@SQ     SN:GL000210.1   LN:27682
@SQ     SN:GL000239.1   LN:33824
@SQ     SN:GL000235.1   LN:34474
@SQ     SN:GL000201.1   LN:36148
@SQ     SN:GL000247.1   LN:36422
@SQ     SN:GL000245.1   LN:36651
@SQ     SN:GL000197.1   LN:37175
@SQ     SN:GL000203.1   LN:37498
@SQ     SN:GL000246.1   LN:38154
@SQ     SN:GL000249.1   LN:38502
@SQ     SN:GL000196.1   LN:38914
@SQ     SN:GL000248.1   LN:39786
@SQ     SN:GL000244.1   LN:39929
@SQ     SN:GL000238.1   LN:39939
@SQ     SN:GL000202.1   LN:40103
@SQ     SN:GL000234.1   LN:40531
@SQ     SN:GL000232.1   LN:40652
@SQ     SN:GL000206.1   LN:41001
@SQ     SN:GL000240.1   LN:41933
@SQ     SN:GL000236.1   LN:41934
@SQ     SN:GL000241.1   LN:42152
@SQ     SN:GL000243.1   LN:43341
@SQ     SN:GL000242.1   LN:43523
@SQ     SN:GL000230.1   LN:43691
@SQ     SN:GL000237.1   LN:45867
@SQ     SN:GL000233.1   LN:45941
@SQ     SN:GL000204.1   LN:81310
@SQ     SN:GL000198.1   LN:90085
@SQ     SN:GL000208.1   LN:92689
@SQ     SN:GL000191.1   LN:106433
@SQ     SN:GL000227.1   LN:128374
@SQ     SN:GL000228.1   LN:129120
@SQ     SN:GL000214.1   LN:137718
@SQ     SN:GL000221.1   LN:155397
@SQ     SN:GL000209.1   LN:159169
@SQ     SN:GL000218.1   LN:161147
@SQ     SN:GL000220.1   LN:161802
@SQ     SN:GL000213.1   LN:164239
@SQ     SN:GL000211.1   LN:166566
@SQ     SN:GL000199.1   LN:169874
@SQ     SN:GL000217.1   LN:172149
@SQ     SN:GL000216.1   LN:172294
@SQ     SN:GL000215.1   LN:172545
@SQ     SN:GL000205.1   LN:174588
@SQ     SN:GL000219.1   LN:179198
@SQ     SN:GL000224.1   LN:179693
@SQ     SN:GL000223.1   LN:180455
@SQ     SN:GL000195.1   LN:182896
@SQ     SN:GL000212.1   LN:186858
@SQ     SN:GL000222.1   LN:186861
@SQ     SN:GL000200.1   LN:187035
@SQ     SN:GL000193.1   LN:189789
@SQ     SN:GL000194.1   LN:191469
@SQ     SN:GL000225.1   LN:211173
@SQ     SN:GL000192.1   LN:547496
@RG     ID:S01N      LB:S01N      PL:ILLUMINA     SM:S01N