Problem with Creating Local Database

[VNF1981]

Hello,

I have successfully created local databases and annotated the whole genome sequences of more than 50 species via SIFT4G. However, I encountered the following issues with four species.

1) I am getting the "Alignment score and position are not consensus" error for one species.

• skipping protein [ rna-XM_016942145.3 ]: substitution list has a position out of bounds (line: M1064I, query length = 1063) *
• skipping protein [ rna-XM_054680350.1 ]: substitution list has a position out of bounds (line: T345T, query length = 344) *
• skipping protein [ rna-XM_054681160.1 ]: substitution list has a position out of bounds (line: E1093D, query length = 1092) *
• processing queries: 100.00/100.00% *

Searching database for candidate sequences

• processing database part 337 (size ~0.25 GB): 100.00/100.00% *

Aligning queries with candidate sequences Alignment score and position are not consensus.7.50/100.00% *

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2) For three species, the process of creating databases breaks without any error during the alignment:

• skipping protein [ rna-XM_016925611.2 ]: substitution list has a position out of bounds (line: S176R, query length = 175) *
• skipping protein [ rna-XM_024345334.2 ]: substitution list has a position out of bounds (line: E348E, query length = 347) *
• skipping protein [ rna-XM_054681488.1 ]: substitution list has a position out of bounds (line: Q138Q, query length = 137) *
• processing queries: 100.00/100.00% *

Searching database for candidate sequences

• processing database part 337 (size ~0.25 GB): 100.00/100.00% *

Aligning queries with candidate sequences

And here is the content of log file:

converting gene format to use-able input done converting gene format making single records file done making single records template making noncoding records file done making noncoding records make the fasta sequences done making the fasta sequences start siftsharp, getting the alignments

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Any advice on these would be highly appreciated in advance!

[pauline-ng]

Congrats on making almost 50 databases!

If you used the gtf file to pull out the underlying DNA sequence for these transcripts, are they valid bases (A/C/G/T) or are there lots of N's?

Because SIFT is translating the DNA into amino acid sequence, and if there are N's, it won't be able to translate it into a protein (and SIFT won't work)

[VNF1981]

Hi Pauline,

The issue has been resolved! I'm not sure what caused it, but I adjusted the method for creating annotations for species that lack them, and now everything is working.

Thanks once again for your quick response!

[pauline-ng]

Great!