Re: [Samtools-help] EOF marker is absent. The input is probably truncated

[Sendu B. <sb...@sa...>]

Actually, in this case the warning should be ignored. Using samtools view -u gives uncompressed bam, and these do not have the EOF marker. 


On 17 Nov 2011, at 14:43, Ivan Gregoretti wrote:
> Hello 王森,
> 
> That means that the bam file has a problem. It is truncated, meaning incomplete.
> 
> Very big files do get corrupted occasionally. You need to create the
> bam file again.
> 
> I hope this helps.
> 
> Ivan
> 
> 2011/11/16 王森 <wa...@bi...>:
>> 
>> 
>> hi,
>> What does this error mean with respect to the completion of my samtools
>> command(samtools sort )?
>> why?
>> [bam_header_read] EOF marker is absent. The input is probably truncated.
>> The commmand:
>> samtools view -buS -T all.fa -o s_5_1.bam s_5_1.sam > log
>> samtools sort -n s_5_1.bam s_5_1.sort > sort.log
>> Thank you!