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7.0 years ago
syseo8819
•
0
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.
What exactly do you mean with "it never worked"? Do you have any output from canu?
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.
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.
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.
Is there a reason why you have canu twice in that command?
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.
What happens if you do
?