Merry Christmas!
On Mon, Dec 25, 2017 at 7:57 PM Hu Jing <hj_hanna2...@hotmail.com> wrote:
> To whom it may concern,
>
>
> Recently we ran into an issue with converting SAM to BAM using samtools
> view command called in python, please see the commands below,
>
>
> cmd = 'samtools view -b -o {} {}'.format(output_BAM, input_SAM)os.system(cmd)
>
>
> The SAM was generated from the Bowtie2, and appended with a few more tags
> defined by our own, such as sequence of UMI (unique molecular index). The
> SAM file is ~4Gb in size. The samtools we're using is version 1.3.1.
>
>
> When we tried to run the above command in a VM with 32Gb RAM, it failed
> silently, and we couldn't see the BAM file generated. After we increased to
> 64Gb RAM, the BAM was generated.
>
>
> Wonder why increasing the RAM could help the conversion of SAM to BAM
> (64Gb is really big compared to the SAM size 4Gb)? Is there any option that
> we may use to print the logs for easier troubleshooting?
>
>
> Thanks so much and happy holidays!
>
> Jing
>
>
>
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