Thanks Bob for the info.
A bit of distraction from samtools bug, I like to mention the reason I wanted
to use sorting here is to allow conversion of bam with paired end reads to
fastq.
I wonder if it would lead to misleading fastq outpur if I convert bam to fastq
without sorting the reads ?
Thanks Collins for ur suggestion of novosort.
> Subject: Re: [Samtools-help] [bam_sort_core] truncated file. Continue anyway
> From: [email protected]
> Date: Fri, 19 Sep 2014 22:37:40 -0400
> CC: [email protected]
> To: [email protected]
>
> As I recall, there's some condition that the decompression library
> incorrectly decides means there's something wrong with the input file, and it
> returns a value that the calling routine can't distinguish from an end of
> file. The calling routine then reports that the file is truncated but
> continues to try to read the rest of the file, and might be successful.
>
> I believe I reported this a few months back but I really got no response from
> the samtools folks. I think/guess the basic problem is that the
> decompression library doesn't originate with this project, so there's
> resistance to making any changes to it. The change I suggested at the time
> *looked* simple enough, but it would involve a change to how that library
> reports errors.
>
> All that may have nothing to do with why your file isn't being sorted though.
>
> Bob H
>
>
> On Sep 19, 2014, at 8:04 PM, Vickie S wrote:
>
>> Hi
>> I am trying to sort the bam file by using the sort command:
>> samtools sort -n aln.bam aln.qsort
>> [W::sam_hdr_read] bgzf_check_EOF: Value too large for defined data type
>> [bam_sort_core] truncated file. Continue anyway.
>>
>> I am not sure if "continue anyway" means it continues to sort or just
>> aborts.
>> I checked the file size.
>> $ du -hs *
>> 113G aln.bam
>> 8.4M aln.bam.bai
>> 28K aln.qsort.bam
>>
>> So it does not seem like file is sorted. I have checked one previous thread
>> about this bug but could not find any solution. Anyone comments ? Suggestion
>> for any other tool ?
>>
>> Thanks
>>
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