Truncated file error

[wzhang1001]

Hello,

I tried to convert bam file to sam using samtools but got the error msg:
truncated file.
samtools view -h -o out.sam in.bam
[main_samview]truncated file

Any idea how to fix this?

Thank you in advance for your help!

[maubp]

If the error message is accurate, your BAM file is truncated. i.e. stops part way through. That can happen if the tool making the BAM file crashed, or you ran out of disk space, or the file was only partially copied, or ...

Check how you made the BAM file didn't give any error/warnings. If you copied the file, check it is the same size as the original.

[TiborNagy]

Samtools read BAM files in default. If you want to read sam files, use -S. Without the -S argument you always get a truncated file error message.