Hello! No matter which tool I try, I cannot seem to be able to obtain a mummer plot. I tried running Mummer, Mummerplot, and MUMmer dotplot, and I always get an error. For Mummer:
Fatal error: Exit code 129 ()
The standard error being :
Reading mummer file /data/jwd06/main/098/526/98526945/outputs/dataset_5684b04c-ed3c-4fe3-ba39-67115b44de34.dat (use mummer -c)
Writing plot files out.fplot, out.rplot, out.hplot
Writing gnuplot script out.gp
Rendering plot out.png
For MUMmer dotplot, I get:
Fatal error: Exit code 1 ()
# reading input file "/data/dnb12/galaxy_db/files/6/3/a/dataset_63ac4be7-b259-47f9-a243-7d1f319e8a0f.dat" of length 34268
# construct suffix tree for sequence of length 34268
# (maximum reference length is 536870908)
# (maximum query length is 4294967295)
# CONSTRUCTIONTIME mummer /data/dnb12/galaxy_db/files/6/3/a/dataset_63ac4be7-b259-47f9-a243-7d1f319e8a0f.dat 0.00
# reading input file "/data/dnb12/galaxy_db/files/9/3/e/dataset_93ed9d89-9ba3-4bf6-b7f3-f4e9568e4e35.dat" of length 67673
# matching query-file "/data/dnb12/galaxy_db/files/9/3/e/dataset_93ed9d89-9ba3-4bf6-b7f3-f4e9568e4e35.dat"
# against subject-file "/data/dnb12/galaxy_db/files/6/3/a/dataset_63ac4be7-b259-47f9-a243-7d1f319e8a0f.dat"
# COMPLETETIME mummer /data/dnb12/galaxy_db/files/6/3/a/dataset_63ac4be7-b259-47f9-a243-7d1f319e8a0f.dat 0.03
# SPACE mummer /data/dnb12/galaxy_db/files/6/3/a/dataset_63ac4be7-b259-47f9-a243-7d1f319e8a0f.dat 0.10
Reading mummer file /data/jwd06/main/098/526/98526972/tmp/tmpKyVr9J/ref_qry.mums (use mummer -c)
Writing plot files /data/jwd06/main/098/526/98526972/tmp/tmpKyVr9J/ref_qry.fplot, /data/jwd06/main/098/526/98526972/tmp/tmpKyVr9J/ref_qry.rplot
ERROR: No alignment data to plot
Error 6400 from: mummerplot -R "/data/dnb12/galaxy_db/files/6/3/a/dataset_63ac4be7-b259-47f9-a243-7d1f319e8a0f.dat" -Q "/data/dnb12/galaxy_db/files/9/3/e/dataset_93ed9d89-9ba3-4bf6-b7f3-f4e9568e4e35.dat" --png --large --prefix=/data/jwd06/main/098/526/98526972/tmp/tmpKyVr9J/ref_qry /data/jwd06/main/098/526/98526972/tmp/tmpKyVr9J/ref_qry.mums
Regarding Mummerplot: when I try to run Nucmer, it completes successfully (when asking for the delta format), but then when I try this as one of the input for Mummerplot, I get the same Fatal error as in Mummer…