sequence and quality are inconsistent

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6.5 years ago

sambioinfo2018 ▴ 20

Hi,

while converting the sam to bam file using samtools i get the following error: [samopen] SAM header is present: 279439 sequences. Parse error at line 31099973: sequence and quality are inconsistent

Below are the commands that i have used for alignment and sam to bam conversion:

bowtie2 -x reference_genome/indexed -1 sample_R1.fastq.gz -2 sample_R2_.fastq.gz -S aligned_PE.sam

samtools view -S -b aligned_PE.sam -o aligned_PE.bam

Could anyone give your suggestion to solve this..

Thanks in advance!!

alignment • 2.9k views

ADD COMMENT • link updated 6.5 years ago by WouterDeCoster 47k • written 6.5 years ago by sambioinfo2018 ▴ 20

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Have you tried looking at the mentioned line (=- few lines) in your original file?. it might be there is a length difference between the two or some 'illegal/hidden' chars have been added?

ADD REPLY • link 6.5 years ago by lieven.sterck 15k

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I have checked that line and there is length difference between the two..

ADD REPLY • link 6.5 years ago by sambioinfo2018 ▴ 20

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You are using a prehistoric version of samtools. 2. Did you consider looking at line 31099973?

ADD REPLY • link 6.5 years ago by John Marshall 3.1k

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I am using samtools 1.3. i looked the line, the difference is there.

ADD REPLY • link 6.5 years ago by sambioinfo2018 ▴ 20

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Are you working with the original files or have they been quality trimmed/filtered and/or merged or something like that?

ADD REPLY • link 6.5 years ago by lieven.sterck 15k

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i am working with quality trimmed files.

ADD REPLY • link 6.5 years ago by sambioinfo2018 ▴ 20

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Then there is a fair chance that something went wrong in the mapping step.

Try to re-run the mapping step (perhaps in verbose mode, so you might spot issues if there are any)

ADD REPLY • link 6.5 years ago by lieven.sterck 15k

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Hi. I have already started re-running alignment step. Thanks!

ADD REPLY • link 6.5 years ago by sambioinfo2018 ▴ 20

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You may have installed samtools 1.3 (which is also somewhat out of date at this point), but if it is printing out "[samopen] SAM header is present" then you are actually using samtools 0.1.18 or thereabouts. Check your $PATH, because you're not using the version of samtools that you think you are.