Why Do I Get "Floating Point Exception" Using Samview Tview ?

Question

[Pascal]

Hi.

I'm getting "floating point exception" error using samtools tview the following way:

$ samtools view -hb ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/data/NA12891/alignment/NA12891.chrom1.ILLUMINA.bwa.CEU.high_coverage.20100517.bam 1:157,200,000-157,300,00 > NA12891.chrom1.ILLUMINA.bwa.CEU.high_coverage.20100517_chr1-157200K-157300K.bam

$ samtools index NA12891.chrom1.ILLUMINA.bwa.CEU.high_coverage.20100517_chr1-157200K-157300K.bam

$ samtools tview NA12891.chrom1.ILLUMINA.bwa.CEU.high_coverage.20100517_chr1-157200K-157300K.bam human_g1k_v37.fasta

I've googled for this error message but I could not find anything similar to this issue.

I have tried to compile samtools source (v0.1.18) on my ubuntu system but it doesn't help.

Where is the bug reporting system for samtools? (I'd like to make sure there is no existing bug and/or workaround).

Am I using the tool is an incorrect way?

Thanks!

Answer 1

[Peter]

Sounds like a bug in samtools, possibly one that has already been fixed (since 0.1.18): http://seqanswers.com/forums/showthread.php?t=14991

Try compiling the latest samtools from the repository, or wait for 0.1.19 to be released.

Answer 2

[Pierre Lindenbaum]

• what is your machine, is it a 32 or a 64 bit machine ?
• the best way to report a bug is the mailing list for samtools: samtools-devel Archives
• Heng Li, one of the core developers of samtools is an active member of Biostar.

[Pascal]

• this is a 64 bit machine
• yes of course, no problem, but prior to report a bug I would like to know to check whether it is actually a bug or if I am using the tool in an incorrect way

[Pascal]

• this is a 64 bit machine

• yes of course, no problem, but prior to report a bug I would like to know to check whether it is actually a bug or if I am using the tool in an incorrect way – Pascal 0 secs ago