SeqChunker: command not found

[Hulanyue]

Hi,thackl! when I run SeqChunker -s 20M -o pb-%03d.fq pb-subreads.fq,there is a problem.

linux@linux-virtual-machine:~/proovread$ SeqChunker -s 20M -o pb-%03d.fq pb-subreads.fq SeqChunker: command not found

linux@linux-virtual-machine:~/proovread$ cd util linux@linux-virtual-machine:~/proovread/util$ SeqChunker -s 20M -o pb-%03d.fq pb-subreads.fq SeqChunker: command not found

linux@linux-virtual-machine:~/proovread/util/SeqChunker/bin$ SeqChunker -s 20M -o pb-%03d.fq pb-subreads.fq SeqChunker: command not found

And I try linux@linux-virtual-machine:~/proovread$ ln -s /home/proovread/util/SeqChunker/bin/SeqChunker-perl ,it is still SeqChunker: command not found

I don't konw what the problem is ,can you enlighten me ?

[greatfireball]

Hey @Hulanyue

seems to be an easy answer: if you call a program or script in Linux, the current folder will not be searched for the program to call. Normally, SeqChunker should be located inside the bin folder. To execute it, just add a bin/ in front of SeqChunker. Therefore your original call should be:

bin/SeqChunker -s 20M -o pb-%03d.fq pb-subreads.fq

Hope that solves your problem.

Best, Frank

PS: If you want to call a program in the same folder use ./ instead a folder name. Moreover, using the absolute path is also always possible. In your case the call would be:

~/proovread/bin/SeqChunker -s 20M -o pb-%03d.fq pb-subreads.fq

[Hulanyue]

Hi @greatfireball Can you tell me what the meaning is about two files(pb-%03d.fq pb-subreads.fq),there are no such files in the folder(I downloaded from this link) and when I run

linux@linux-virtual-machine:~/proovread/util/SeqChunker$ bin/SeqChunker -s 20M -o pb-%03d.fq pb-subreads.fq FILE should be located at 'bin/SeqChunker' The file 'pb-subreads.fq' does not exist!

I try to use other file(.fq) to replace pb-subreads.fq,it is still does not exist!

[greatfireball]

Sure, the -o pb-%03d.fq defines the name of the output files. Within the expression %03d is a placeholder and will be substituted by (at least) three digit numbers with leading zeros. The pb-subreads.fq is the input file. If the input file does not exist, just use one existing. If the file is not located inside the current directory, you can specify its location via a relative or an absolute path, eg. ../data/in.fq will search for a file in a subfolder called data of the current parent directory names in.fq. As already mentioned, you can use absolute paths as well, eg. ~/proovread/data/in.fq.

[Hulanyue]

when I run bin/SeqChunker -s 20M -o pb-%03d.fq ~/proovread/util/SeqChunker/t/ec.fq,it shows me : linux@linux-virtual-machine:~/proovread/util/SeqChunker$ bin/SeqChunker -s 20M -o pb-%03d.fq ~/proovread/util/SeqChunker/t/ec.fq FILE should be located at 'bin/SeqChunker' Reading /home/linux/proovread/util/SeqChunker/t/ec.fq

I don't know whether it is right ,because it shows me FILE should be located at 'bin/SeqChunker' But, at least a file(pb-001.fq) was generated.

[greatfireball]

Does it contain the sequences from ec.fq? That would be fine. Nevertheless, you should probably call bin/SeqChunker -s 20M -o pb-%03d.fq ~/proovread/util/SeqChunker/t/ec.fq from the folder ~/proovread/.

[Hulanyue]

Yes,two files are same! Thank you very much,frank!!

[greatfireball]

Welcome... Just let us know, if you need further help