Canu assembler scripts

Question

[syseo8819]

I have a huge problem to run Canu assembler in the server. I made a script and run it. But, it never worked.

My command lines are like this;

canu useGrid=0 canu -p test -d ~/Genome_Assembly genomeSize=500000 -pacbio-raw ~/Genome_Assembly/test89.fastq

I have tried several time such as I add the path of the input file or options of '-p' or '-d'. Please give me any advice. Thanks.

[cschu181]

What exactly do you mean with "it never worked"? Do you have any output from canu?

[syseo8819]

Thanks for replying my question. It means I have never seen output files. As soon as I had submitted my script in my server, the job was just finished after a few seconds. Here is error messages from the server; ERROR: Assembly name prefix not supplied with -p. ERROR: Directory not supplied with -d. ERROR: Invalid 'corErrorRate' specified; must be set ERROR: Required parameter 'genomeSize' is not set Please help me.

[cschu181]

Can you tell me what you typed on the command line in order to run canu? It looks as if you're missing all the non-optional input parameters.

[syseo8819]

Thanks for answering my question again! I typed "run_script canu.sh" in command line, because I use the server which already has a canu program and I just need to load modules. Also, I made a script which is named as canu.sh.

#!/binsh load/modules/command/lines canu useGrid=0 canu -p test -d test genomeSize=500000 -pacbio-raw test89.fastq I really appreciate you.

[cschu181]

Is there a reason why you have canu twice in that command?

[syseo8819]

That's why when I asked about my script to the manager of the server which I have usually used, he said that I need to make the false parameter of grid in their server. But, even though the first canu command didn't exist, the script was not working at all. Thanks.

[cschu181]

What happens if you do

canu useGrid=0 -p test -d test genomeSize=500000 -pacbio-raw test89.fastq

?