ACT: Comparison file read failed error

Question

[sarah_27_m]

Hello,

I am trying to generate comparison files (crunch files) to view in ACT. I am using the example code below in the terminal:

makeblastdb -in NC_011748.fasta -dbtype nucl

blastn -query SRR292770_single.fasta -db NC_011748.fasta -evalue 1 -task megablast -outfmt 6 > SRR292770_NC_011748.crunch

I am able to generate the crunch files using the my fasta files but when I try to load my .gbk file into ACT i get the following message:

"comparison file read failed: out of range error: match goes off end of query sequence 319884

I am successful when I load my crunch file with my seq.fasta file and the reference.gb file (downloaded from NCBI) however I get the aforementioned error message using the .gbk file that I received from MicrobesNG

Thanks Sarah

[Mensur Dlakic]

It appears that the two GenBank files are different. Specifically, it seems that a file from MicrobesNG is shorter. If this is the file you need, convert it to FASTa, do the search with it, and it should work afterwards. Alternatively, go with whatever works already.