Closed Astahlke closed 3 years ago
Hi Amanda,
can you generate a self alignment of the canu contig selected by mitoVGP (or attach the fasta from canu). Usually this is very informative of repeats and other structures that may cause issues to mummer. We can increase the processivity of mummer with the option -z (e.g. 5000 could be a good value), if the problem is just finding the overlap within a nasty repeat.
I am closing since it's duplicated
Hello!
Looking for help resolving the trimmer module of the mitovgp pipeline. The first trimmer script is not completing. From what I can tell there's no error generated. It appears that mummer successfully runs twice, but the expected ${FNAME}_polish2_10x1_trim1.fasta isn't generated at the end for map10x2 to proceed. Any suggestions to resolve this?
Here's the relevant standard output:
I've attached a couple of other log files here - not sure what's most helpful. Thanks in advance for any ideas. I've posted this same issue at https://github.com/gf777/mitoVGP/issues/1
Pgos_mtDNApipe_20210624-174115.log Pgos_trimmer_20210624-222455.log R-mtpipe.6056486.err.log R-mtpipe.6056486.out.log
Amanda