SPAdes error "Missing @SQ header"

Question

[Angelo Victoria]

Hi!

I am trying to do a de-novo assembly of a prokaryotic genome using SPAdes 3.5.0. I have been getting the following error

[samopen] no @SQ lines in the header.

[sam_read1] missing header? Abort!

I tried doing a subset of the reads and it worked. Thinking that it was a memory issue, I increased the memory allocation from 128GB to 350GB to give it ample memory but, unfortunately, it still didn't work with the full data set.

I think it has something to do with the mismatch correction (--careful) because the assembly was finished but the correction was aborted.

It also created a file named "@SQ SN:NODE_87368_length_231_cov_2.38312_ID_174735 LN:231" in the home directory (outside the spades folder), if that would be of any help.

Thanks!

Answer 1

[Philipp Bayer]

In --careful, Spades uses BWA to align the reads back to the assembly in order to correct minor indels. This step generates the BAM files about which it complains.

There's a good chance that this breaks for your for some reason - could you post the whole STDOUT to pastebin.com or something like that? I have a hunch there's a tiny BWA error hidden somewhere, so that the BAM file isn't generated correctly, maybe there's a bogus read in the whole dataset, etc.