[main_samview] fail to read the header from sample.bam

Question

[sambioinfo2018]

Hi all, I get the following error when reading the sample.bam. The file was converted from sam to bam using the following command:

 samtools view -bS sample.sam > sample.bam.

[E::bgzf_read] bgzf_read_block error -1 after 194938 of 8572040 bytes
[E::bam_hdr_read] error reading BGZF stream
[main_samview] fail to read the header from sample.bam

Looking forward to get your suggestion.

thanks in advance

sam

[GenoMax]

Does your sam file have a valid header? If yes, then have you tried reconverting the file? Perhaps something happened to corrupt the file first time around.

[sambioinfo2018]

Yes, a valid header is present in sam file. I could not understand about reconverting?

[ATpoint]

What is the output of:

samtools view -H sample.sam
samtools quickcheck -v sample.sam

[sambioinfo2018]

while running samtools view -H sample.sam, it result is following: [main_samview] fail to read the header from sample.sam

[GenoMax]

That is your problem then. With what program was the sam file generated?

[sambioinfo2018]

When i looked the same file with head command i could see the first 10 header lines. However with the above command its showed as failed to read. I have rerun the alignment once again. And now its reading the sam file. Thanks!! Shall convert to bam file now.

[sambioinfo2018]

i have also tried converting using samtools view -h -b sample.sam > sample.bam

[rturba]

I am having a similar issue. I'm following the CapSim tutorial, and when I'm trying to run this command:

samtools view -bSU probes.sam | samtools sort -o probes.bam -

I'm getting the error:

samtools sort: failed to read header from "-"

I have checked the file header with the commands above, and I do see it:

[rturba@n1848 aDNA]$ samtools view -H probes.sam
@HD     VN:1.0  SO:unsorted
@SQ     SN:KF030964.1   LN:15653
@PG     ID:bowtie2      PN:bowtie2      VN:2.4.2        CL:"/u/local/apps/bowtie2/2.4.2/bowtie2-align-s --wrapper basic-0 --local --very-sensitive-local --mp 8 --rdg 10,8 --rfg 10,8 -k 10000 -f -x anatina -S probes_anatina.sam -U baits-80-20.fa"
@PG     ID:samtools     PN:samtools     PP:bowtie2      VN:1.11 CL:samtools view -H probes_anatina.sam
[rturba@n1848 aDNA]$ samtools quickcheck -v probes.sam
[rturba@n1848 aDNA]$

So what am I doing wrong here?

[ATpoint]

Probably you are using an ancient samtools version that did not have the -o option yet. Output of samtools --version?

[rturba]

It's samtools v1.11. Sorry, I should've added that. Does that mean I have to do the > then?

[ATpoint]

No, that should be fine with v1.11. I just see that there is -U (capital U) rather than -u in view. That is probably wrong. You do not need view anyway, sort can read a SAM file directly and output bam.

[Jorge Amigo]

That's exactly the problem: The -U option is to Output reads not selected by filters to FILE, but the option you want is the -u to get Uncompressed BAM output, which already implies -b so you don't need to specify it. Also, the -S option to indicate that your input is SAM rather than BAM is deprecated, but samtools doesn't complain if you use it. samtools view -u probes.sam should be enough to feed any tool that would need a probes.sam in BAM format.

ATpoint you're right about not having to use a previous samtools view in order to convert SAM to BAM, as samtools sort already understands SAM, BAM and CRAM inputs. Online documentation does state this, although unfortunately samtools's man page doesn't.

[Qboy]

Hey, I have one question.

What does an empty flag mean after probes.bam

Thank you!

Answer 1

[Kevin Blighe]

The error messages indicate that the BAM file is likely truncated or corrupted during the conversion process. This can occur when using output redirection with the greater-than symbol in the command, as it may not handle large files properly or could be interrupted.

To resolve this, reconvert the SAM file to BAM using the recommended output flag instead of redirection. Run the following command:

samtools view -b -o sample.bam sample.sam

After conversion, verify the integrity of the new BAM file by checking its header:

samtools view -H sample.bam

If this succeeds without errors, the file is readable. Additionally, you can sort and index the BAM file for further use:

samtools sort -o sample.sorted.bam sample.bam
samtools index sample.sorted.bam

If the error persists, inspect the original SAM file for completeness by checking its size and ensuring it was not truncated during download or transfer. You may also need to redownload or regenerate the SAM file.

Kevin