Hey guys,
Recently, I was trying to identify homologous genes in different genomes using genBlastG, however when I run it with default parameters, it generates a huge (~4G) empty output file (.gblast extension with other string attached, i.e., XX.gblast_1.1c_2.3_s1_0_16_1). Other intermediates file seems right, such as .blast and .report files.
I tried so many times with various modifications but the problem still exists. Does anyone know about this problem?
Many Thanks!
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written
by
taylorzheng.zz •
2 answers
Hey, I was trying to install GenBlastA and G by conda ,after installing, I try to use 'genblast' command, but it respond that 'command not found'. Can you tell me how did you install it？
yes. I have activate conda environment. And then I typed 'genblasta' or 'genblast'. Still not found this command.
Hey!
you can download it with wget http://genome.sfu.ca/genblast/latest/genblasta_v1.0.4_linux_x86_64. Then chmod 755 genblasta_v1.0.4_linux_x86_64.Now you can easily run it with ./genblasta_v1.0.4_linux_x86_64.
It is not necessary to install it with conda.
Hope it is helpful.
This link gives a 404 error now. Anyone know where else it might be found?
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Hey, I also met the same problem, but I found it is not the empty file, I filter the output file with
grep '^MY_FASTA_ID' output_file | less, waiting for a moment, and then you can see the file name. I do not know whyless output_filecannot see the contents. The method works for me. Hope it is helpful! BTW, do you know why the output file is so huge? My hard drive is almost full...