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[samopen] SAM header is present: xxx sequences.

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

samtools sam bam
• 8,058 views • link
updated by Ram Ram • written by noushin.farnoud noushin.farnoud

1 answer

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

• 0 views • link
updated by Ram Ram • written by Brian Bushnell Brian Bushnell

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

• 0 views • link
updated by Ram Ram • written by noushin.farnoud noushin.farnoud

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.

• 0 views • link
updated by Ram Ram • written by Brian Bushnell Brian Bushnell

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

• 0 views • link
updated by Ram Ram • written by noushin.farnoud noushin.farnoud

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