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eead-csic-compbio / get_homologues

GET_HOMOLOGUES: a versatile software package for pan-genome analysis
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COGreadblast produce empty results #106

Closed RiversDong closed 1 year ago

RiversDong commented 1 year ago

I am using COG making algorithm to produce my own ortholog group for more than 100 genomes. According to readme reporting at COGsoft.201204/Readme.2012.04.txt downloaded at https://ftp.ncbi.nih.gov/pub/wolf/COGs/COGsoft/COGsoft.201204.tar. I encountered a confusion when using COGreadblast. This program produced empty results for self.csv, query2subject.csv and hits.csv.

Here are the details: Command: COGreadblast -d=/home/chuand/giant_virus/result/BLASTconv -u=/home/chuand/giant_virus/result/BLASTno -f=/home/chuand/giant_virus/result/BLASTff -s=/home/chuand/giant_virus/result/BLASTno -e=0.1 -q=2 -t=2

The blast results (BLASTno.tab and BLASTff.tab) were stored in /home/chuand/giant_virus/result/BLASTno, and /home/chuand/giant_virus/result/BLASTff. Format looks like as following: image

The format of hash.csv looks like image

eead-csic-compbio commented 1 year ago

Hi @RiversDong , this is not a GET_HOMOLOGUES question. However, I suggest you run get_homologues.pl -G with (a subset of) your data and see how the files are formatted for COG, Bruno

RiversDong commented 1 year ago

Thanks for your kindly help. This is very helpful