[E::hts_idx_push] Unsorted positions on sequence #...

[M. Alicia Pascual R.]

Hi,

I have used dDocent in the past with the same samples (paired reads from GBS) and everything ran smoothly. Turns out there is a new reference genome that I was not aware of and so I have to map my reads to that one (which I just downloaded from NCBI) instead of assembling my own, as I had done. And here is where I have encountered problems. After quality filtering I seem to be having problems while mapping. This is the last error:

Using BWA to map reads

[E::hts_idx_push] Unsorted positions on sequence #298: 7801 followed by 7477

samtools index: failed to create index for "1c_244-RG.bam"

samtools index: failed to create index for "cat-RRG.bam"

Error: Sorted input specified, but the file cat-RRG.bam has the following out of order record

QFDD01000298.1  7476    7572    K00243:191:HGJNLBBXY:5:1101:25926:1226/2        60      +

*****

***** ERROR: Requested column 4, but database file - only has fields 1 - 0.

Using FreeBayes to call SNPs

ls: cannot access 'mapped.*.bed': No such file or directory

0% 0:0=0s                                                                                                                                    

rm: cannot remove 'mapped.*.bed': No such file or directory

could not open "raw.*.vcf" exiting

mv: cannot stat 'raw.*.vcf': No such file or directory

Using VCFtools to parse TotalRawSNPS.vcf for SNPs that are called in at least 90% of individuals

mawk: cannot open ./logfiles/VCFtools.log (No such file or directory)

Thanks,

M

[Jon Puritz]

My gut feeling is this has to due with weird characters introduced by NCBI.  I would double check that there isn't anything funny looking in the reference file.

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