KeyError in get_contigs_border.py

[maherrl]

Hello,

I am trying to run get_contigs_border.py and get a KeyError for the first contig name in my orderings.txt file:

[rmaher@node03 ragoo_output]$ ../../../scripts/get_contig_borders.py orderings/orderings.txt ragoo.fasta.fai 100
Traceback (most recent call last):
  File "../../../scripts/get_contig_borders.py", line 36, in <module>
    end = current_pos + ctg_lens[ctg]
KeyError: 'contig_1519_pilon'

[rmaher@node03 ragoo_output]$ head orderings/orderings.txt 
contig_1519_pilon	+	0.0007311710909015015	1.0
contig_7014_pilon	-	1.0	1.0
contig_7501_pilon	-	1.0	1.0
contig_8402_pilon	+	0.7593714066692219	1.0
contig_4502_pilon	-	0.020602532576925483	0.8634162743779422
contig_2013_pilon	+	0.03029503412896441	1.0
contig_5648_pilon	+	1.0	1.0
contig_7753_pilon	+	0.06289335411975287	1.0
contig_7868_pilon	-	1.0	1.0
contig_6766_pilon	-	0.06796488354117877	0.70093214262434

Any idea what could be going wrong here?

[malonge]

Hi there,

Looks like you passed the fai file for the pseudomolecules (ragoo.fasta). Instead, please try passing the fai for you input contigs (the contigs that comprise the pseudomolecules).

Thanks