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.