Problem with Mummer

usegalaxy.eu support
1

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…

1 Like
2

Hi @davidjoly

Yes, I can reproduce the problems. I’ve reported this to the UseGalaxy.eu administrators. I would suggest that you send in examples from your errors as well using the :beetle: bug icon from the red error datasets. This is mostly to provide them with the full range of user impact, not necessarily to get this “reported” in full (instead, I’ll be helping with this part). FAQ: Troubleshooting errors

I’ll be creating a ticket later today (after a few more technical tests) and will post back the tracking ticket. The issue impacts all of the UseGalaxy servers.

As a temporary workaround, you could move into a Jupyter Notebook environment, install the tool, and run it inside of there. → GTN Materials Search (query=jupyter).

Thanks for reporting the problem! We’ll know more about the scope and timeline later. More soon! :slight_smile: