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Old 04-29-2009, 09:33 AM   #1
AnamikaDarwin
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Location: Boston

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Question Samtools Pileup Assertion Error

Hello,

I am trying to use the samtools pileup command with the -c and -f flags to get the consensus sequnce, but am getting an error.


Command : samtools pileup -c -f RefAssemb.fasta Ref_Reads.aligned.bam
Error message: [fai_load] build FASTA index. samtools: faidx.c:171: fai_build: Assertion `fp' failed. Abort.


Has anybody else encountered the above error? And how did you resolve the same?

Thanks,
Anamika
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Old 06-17-2009, 01:06 PM   #2
xguo
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Anamika,

I got the same error "samtools: faidx.c:171: fai_build: Assertion `fp' failed. Abort.". Have you figured out how to solve this error?

thanks
Xiang
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Old 06-29-2009, 12:44 PM   #3
AnamikaDarwin
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Quote:
Originally Posted by xguo View Post
Anamika,

I got the same error "samtools: faidx.c:171: fai_build: Assertion `fp' failed. Abort.". Have you figured out how to solve this error?

thanks
Xiang
Hi Xiang,

My issue got resolved after I indexed the reference assembly by running the command
samtools faidx ref.fasta.

~Anamika
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