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KeyError in get_contigs_border.py #60

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maherrl opened this issue Apr 21, 2020 · 1 comment
Open

KeyError in get_contigs_border.py #60

maherrl opened this issue Apr 21, 2020 · 1 comment

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@maherrl
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maherrl commented Apr 21, 2020

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
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malonge commented Apr 23, 2020

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

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