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Old 07-11-2013, 02:20 PM   #1
akjones
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Location: North America

Join Date: Jun 2013
Posts: 24
Question Using PROmer as part of ABACAS (PAGIT)

Hi all,

I have recently installed PAGIT on Mac OSX and am working with ABACAS. So far I have gotten abacas to run using the default parameter settings and NUCmer. The command I entered was $PAGIT_HOME/ABACAS/abacas.pl -r Ddesulfuricans132.fasta -q Stringentcontigs_avg_cvg10orgreater.fa -p nucmer -m -b -o firstrun (where Ddesulfuricans132.fasta and Stringentcontigs_avg_cvg_10orgreater.fa are my reference and query, respectively), this worked fine and generated the expected result files. I wanted to try using PROmer instead of NUCmer and entered the same command as above, only this time using PROmer after the "-p" flag and changing the output prefix. It did not work and I got this error message: ERROR: Could not parse delta file, promer.delta
error no:400

I have no idea what that means, I tried Googling the error (high tech, I know) and couldn't find anything useful. Any thoughts or suggestions? I would greatly appreciate it. Also as an fyi, I am very much a beginner with bioinformatics in general and especially with running programs in Unix or Linux command line. Please keep that in mind with feedback.

Thanks,
~akjones
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