Question: Canu assembler scripts
0
gravatar for syseo8819
20 months ago by
syseo88190
syseo88190 wrote:

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.

canu assembly • 934 views
ADD COMMENTlink written 20 months ago by syseo88190

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

ADD REPLYlink written 20 months ago by cschu1811.4k

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.

ADD REPLYlink written 20 months ago by syseo88190

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.

ADD REPLYlink written 20 months ago by cschu1811.4k

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.

ADD REPLYlink modified 20 months ago • written 20 months ago by syseo88190

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

ADD REPLYlink written 20 months ago by cschu1811.4k

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.

ADD REPLYlink written 20 months ago by syseo88190

What happens if you do

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

?

ADD REPLYlink written 20 months ago by cschu1811.4k
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