Unable to annotate SNP using both kSNP3/kSNP4

[Brad Yang]

Hi all,

I have tried to use kSNP3/kSNP4 to annotate SNP but both fail to do so. The annotation summary in kSNP3 is empty while it shows those core SNPs are not in annotated . kSNP4 doesn't give me any error message and kSNP3 generated the following:

headers.annotate_list: headers.annotate_list
annotate_list: annotate_list
genbank files: genbank_from_NCBI.gbk
$all_snps_file: SNPs_all
$redundant_annotations 0
SNP_annotations file: SNP_annotations
SNPs_all_annotated: SNPs_all_annotated
SNPs_all
Finished SNP annotation.
Traceback (most recent call last):
File "ParAnn.py", line 298, in <module>
KeyError: 'AALXFI010000002.1'
Failed to execute script ParAnn
Finished running kSNP</module>

FYI, AALXFI010000002.1 is the name of the first contig in my reference genome. I have a total of 80 genomes. They are all fasta files and stored in one folder. One of them is used as a reference. In my annotated_list, it is just the name of that fasta (everything excluding .fasta). kSNP3_In_File includes information for all 80 genomes.

Here is the command I use:
kSNP3 -in kSNP3_In_File -outdir kSNP3_Output -k 19 -core -min_frac 0.9 -CPU 40 -annotate annotated_list -vcf

I have previously used kSNP3 to construct the core SNP matrix and don't have any issue. Not sure why annotation doesn't work. Please let me know what you think.

Thanks,
Brad

[Barry G. Hall]

Brad,
Email me directly at barryghall@gmail.com for assistance.

Barry G. Hall
Director, Bellingham Research Institute
barryghall@gmail.com
http://www.bellinghamresearch.com http://www.bellinghamresearch.com/

On May 31, 2023, at 3:01 PM, Brad Yang ly276@users.sourceforge.net wrote:

Hi all,

I have tried to use kSNP3/kSNP4 to annotate SNP but both fail to do so. The annotation summary in kSNP3 is empty while it shows those core SNPs are not in annotated . kSNP4 doesn't give me any error message and kSNP3 generated the following:

headers.annotate_list: headers.annotate_list
annotate_list: annotate_list
genbank files: genbank_from_NCBI.gbk
$all_snps_file: SNPs_all
$redundant_annotations 0
SNP_annotations file: SNP_annotations
SNPs_all_annotated: SNPs_all_annotated
SNPs_all
Finished SNP annotation.
Traceback (most recent call last):
File "ParAnn.py", line 298, in <module>
KeyError: 'AALXFI010000002.1'
Failed to execute script ParAnn
Finished running kSNP</module>

FYI, AALXFI010000002.1 is the name of the first contig in my reference genome. I have a total of 80 genomes. They are all fasta files and stored in one folder. One of them is used as a reference. In my annotated_list, it is just the name of that fasta (everything excluding .fasta). kSNP3_In_File includes information for all 80 genomes.

Here is the command I use:
kSNP3 -in kSNP3_In_File -outdir kSNP3_Output -k 19 -core -min_frac 0.9 -CPU 40 -annotate annotated_list -vcf

I have previously used kSNP3 to construct the core SNP matrix and don't have any issue. Not sure why annotation doesn't work. Please let me know what you think.

Thanks,
Brad

Unable to annotate SNP using both kSNP3/kSNP4 https://sourceforge.net/p/ksnp/discussion/general/thread/66d43bdbe4/?limit=25#72fb
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