speedseq var error

[bioxu]

Hi, I have aligned the sequence used speedseq align commad,but when I use speedseq var, error is exist quickly. Commad:speedseq var -o ERS189473 -w -t 12 /share/disk1/xujt/software/SpeedSeq/speedseq/annotations/ceph18.b37.include.2014-01-15.bed /share/disk1/xujt/data/human_genome/GRCh37/human_g1k_v37.fasta.gz ERS189473.bam

Error: signal 11: /share/disk1/xujt/software/SpeedSeq/speedseq//bin/freebayes[0x4976e3] /lib64/libc.so.6[0x3da4e326a0] /share/disk1/xujt/software/SpeedSeq/speedseq//bin/freebayes[0x451898] /share/disk1/xujt/software/SpeedSeq/speedseq//bin/freebayes[0x4534f9] /share/disk1/xujt/software/SpeedSeq/speedseq//bin/freebayes[0x40822c] /lib64/libc.so.6(__libc_start_main+0xfd)[0x3da4e1ed5d] /share/disk1/xujt/software/SpeedSeq/speedseq//bin/freebayes[0x407a19]

What can I do for it? Thanks for your reply.

[cc2qe]

this looks like a problem with the Freebayes installation. If you run /share/disk1/xujt/software/SpeedSeq/speedseq//bin/freebayes -h can you verify that it's compiled properly?

[bioxu]

Thanks, when I ran the command, the help information is following, I think it's complied properly.

usage: freebayes [OPTION] ... [BAM FILE] ...

Bayesian haplotype-based polymorphism discovery.

citation: Erik Garrison, Gabor Marth "Haplotype-based variant detection from short-read sequencing" arXiv:1207.3907 (http://arxiv.org/abs/1207.3907)

overview:

 To call variants from aligned short-read sequencing data, supply BAM files and
 a reference.  FreeBayes will provide VCF output on standard out describing SNPs,
 indels, and complex variants in samples in the input alignments.

 By default, FreeBayes will consider variants supported by at least 2
 observations in a single sample (-C) and also by at least 20% of the reads from
 a single sample (-F).  These settings are suitable to low to high depth
 sequencing in haploid and diploid samples, but users working with polyploid or
 pooled samples may wish to adjust them depending on the characteristics of
 their sequencing data.

 FreeBayes is capable of calling variant haplotypes shorter than a read length
 where multiple polymorphisms segregate on the same read.  The maximum distance
 between polymorphisms phased in this way is determined by the
 --max-complex-gap, which defaults to 3bp.  In practice, this can comfortably be
 set to half the read length.

 Ploidy may be set to any level (-p), but by default all samples are assumed to
 be diploid.  FreeBayes can model per-sample and per-region variation in
 copy-number (-A) using a copy-number variation map.
 FreeBayes can act as a frequency-based pooled caller and describe variants
 and haplotypes in terms of observation frequency rather than called genotypes.
 To do so, use --pooled-continuous and set input filters to a suitable level.
 Allele observation counts will be described by AO and RO fields in the VCF output.

......... ......... .........

[cc2qe]

Oh, I think I may see a problem with your command: the -w should be followed by the bed file. Looks like the arguments are out of order