Question: [samopen] SAM header is present: xxx sequences.
1
gravatar for noushin.farnoud
4.5 years ago by
United States
noushin.farnoud100 wrote:

Hi,

I am using the line below to convert SAM to BAM and then sort them:

samtools view -bS $mySAM | samtools sort -n -m 6000000000 - $myBAM

Eventhough the process seem to be generating an output, I receive the following log:

[bam_header_read] EOF marker is absent. The input is probably truncated.
[samopen] SAM header is present: 211 sequences.

Is the fact that I am inputting an aligned RNASeq.sam file and it indicates that 211 sequences have SAM header something I need to worry about?

I appreciate your feedback,

Thanks,
Noushin

 

 

 

sam samtools bam • 4.1k views
ADD COMMENTlink modified 4.5 years ago by Brian Bushnell16k • written 4.5 years ago by noushin.farnoud100
3
gravatar for Brian Bushnell
4.5 years ago by
Walnut Creek, USA
Brian Bushnell16k wrote:

The "EOF marker is absent" line is a bug in samtools that always occurs when using piped input.  Just ignore it.

ADD COMMENTlink written 4.5 years ago by Brian Bushnell16k

Thanks a lot Brian! Is it also normal that only 211 sequences in SAM file appear to have SAM headers?

ADD REPLYlink written 4.5 years ago by noushin.farnoud100
3

The number of sequences with headers depends on the reference, not the reads.  So for example if you are working with the human genome, excluding auxiliary stuff like unplaced contigs, samtools will report 25 sequences - 22 autosomes, 2 sex chromosomes, and one mitochondrial sequence.  This is a result of the reference, and independent of your reads.

ADD REPLYlink written 4.5 years ago by Brian Bushnell16k

Thank you very much for clarifying! That totally makes sense now. 

ADD REPLYlink written 4.5 years ago by noushin.farnoud100
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