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Old 05-26-2013, 05:03 PM   #1
wangli
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Location: Texas

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Default samtools mpileup error

samtools mpileup -C50 -I -ugf -R myReference.fa myInput.bam | bcftools view -bvcg - > samtoolsSNPs.raw.bcf

[fai_load] build FASTA index.
open: No such file or directory
[_razf_open] fail to open -R
[fai_build] fail to open the FASTA file -R
[fai_load] fail to open FASTA index.
[afs] 0:0.000

I checked for more than one time to make sure that I have the reference.fa.fai and reference.dict files. So I donot know why the error still shows up.

Any idea?
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Old 05-26-2013, 05:37 PM   #2
win804
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Please remove the "-R" from your command line and try again.

samtools mpileup -C50 -I -ugf myReference.fa ........
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Old 05-28-2013, 06:55 AM   #3
wangli
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It works when removing -R flag. Thank you, win804!
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