Samtools Pileup Assertion Error

[AnamikaDarwin]

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

[xguo]

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

[AnamikaDarwin]

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