genBlastA output file .gblast error

Question

[taylorzheng.zz]

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!

[washion215]

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 why less output_file cannot 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...

Answer 1

[biomonte]

In my case, this problem was solved by renaming IDs of the query sequences to something short and not very complex (avoid semicolons, vertical bars, etc.). I am not sure exactly what caused the issue thought.

Answer 2

[1050446364]

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？

[Tm]

After installation, have you activated the conda environment for GenBlastA? like:

conda activate genblasta

[1050446364]

yes. I have activate conda environment. And then I typed 'genblasta' or 'genblast'. Still not found this command.

[washion215]

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.

[jaredbernard]

This link gives a 404 error now. Anyone know where else it might be found?