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error during shotmap.pl #5
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The file in question (shotmap_db_nr_seqeunce_lengths.tab) is present in the folder where the shotmap database is present, but for some reason the "Calculating abundance.." step was looking for the file in the shotmap_output folder?? |
Hi Ameet, We recently stumbled across this bug and fixed it. You should be able to
If shotmap_tests_log.txt finishes without an error, then this bug should be That said, because I don't want you to have to rebuild your search database
Once I've been able to confirm that everything is properly configured, Sorry for the trouble. Best, On Mon, Mar 7, 2016 at 11:58 AM, ameetpinto notifications@github.com
Thomas J. Sharpton Assistant Professor (541) 737-8623 |
Thanks Tom. This is very helpful! I will give this a try and let you know how it goes. Thanks again for being so responsive with this. Much appreciated. From: Thomas Sharpton <notifications@github.commailto:notifications@github.com> Hi Ameet, We recently stumbled across this bug and fixed it. You should be able to
If shotmap_tests_log.txt finishes without an error, then this bug should be That said, because I don't want you to have to rebuild your search database
Once I've been able to confirm that everything is properly configured, Sorry for the trouble. Best, On Mon, Mar 7, 2016 at 11:58 AM, ameetpinto <notifications@github.commailto:notifications@github.com>
Thomas J. Sharpton Assistant Professor (541) 737-8623 — |
My pleasure, and apologies for the hiccup. Do let me know how I can help, Best of luck, On Tue, Mar 8, 2016 at 11:24 AM, ameetpinto notifications@github.com
Thomas J. Sharpton Assistant Professor (541) 737-8623 |
Hi,
I ran the following command and encountered an error.
perl /home/opt/shotmap/scripts/shotmap.pl -i shotmap_input/ -d shotmap -o shotmap_output/ --nprocs 20 --class-score=35 --postrare-samps=69423326 --rarefaction-type=read
From what I can tell it successfully ran prodigal, rap search, and microbecensus on all four samples that I used for this analyses. It generated an error while "Calculating Abundances". The error was that it could not find the file: shotmap_db_nr_seqeunce_lengths.tab in the parameters folder. See attached snapshot of the error. Any suggestions on how to fix this issue?
Thanks again for your help,
Ameet
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