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wangna62691 / PacBio_Assembly

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canu #2

Open wangna62691 opened 7 years ago

wangna62691 commented 7 years ago

Check in script to your class GitHub repository and run on zcluster

Open new issue on class GitHub repository recording link to Canu script, exact command used to submit job, and GitHub revision of script used https://github.com/wangna62691/PacBio_Assembly.git

qsub -q rcc-30d -l mem_total=8g -pe thread 4 ./canu.sh

https://github.com/wangna62691/PacBio_Assembly/blob/master/canu

provide link to annotation script

https://github.com/wangna62691/PacBio_Assembly/blob/master/prokka.sh

record exact command used to submit job on zcluster

qsub -q rcc-30d ./prokka.sh

record GitHub revision of script used

https://github.com/wangna62691/PacBio_Assembly/blob/a07ba2122103e86e13fc84a1e5c645e9d0535860/prokka.sh

report how many genes you found and compare to U00096

There are 5792 CDS in the file, when I ran U00096 in prokka, the results show that U00096 has 4305 genes.

cbergman commented 7 years ago

Concerning the prokka analysis: you haven't recorded your github version (you only link to the master branch, which has changed since you submitted your jobs). Also, you haven't done this work in your scratch directory.

In the future, please use a new comment for new work rather than editing an old comment. Edits don't send a notification to me that you've submitted your work. Thanks!