edgardomortiz / sam2consensus Goto Github PK

Hi,

I tried to pull an consensus from an Minimap2 Alignment. sam2consensus stops with the following error message:
lars@helmut:~/Desktop/VZV/Carina_09_2021/VZV_ORF14_cmv/assembly-test/Scaffold$ python /home/lars/Desktop/NGS/sam2consensus-master/sam2consensus.py -f N -p final -i scaffold_mapping.sam

Processing file scaffold_mapping.sam:

SAM header processed, 1 references found.

0 reads processed.
Traceback (most recent call last):
File "/home/lars/Desktop/NGS/sam2consensus-master/sam2consensus.py", line 430, in
main()
File "/home/lars/Desktop/NGS/sam2consensus-master/sam2consensus.py", line 212, in main
sequences[refname][pos_ref][nuc] += 1
KeyError: '*'

The .sam file seemed to be correct. There are no issues while importing and visualize it in CLC or Geneious.

Best,

Lars