Question: MUMmer dot plot error
0
gravatar for k.mamoud
2.9 years ago by
k.mamoud30
Switzerland
k.mamoud30 wrote:

Dear all,

I have installed into my local Galaxy the tool Mummer dot plot, I have an error that  I can't understand for the option mummer search algorithm when I am using mummer i have this error :

Fatal error: Exit code 1 ()
# reading input file "/home/galaxy/Galaxy_data_repository/files/001/dataset_1509.dat" of length 2403545
# construct suffix tree for sequence of length 2403545
# (maximum reference length is 536870908)
# (maximum query length is 4294967295)
# process 24035 characters per dot
#....................................................................................................
# CONSTRUCTIONTIME mummer /home/galaxy/Galaxy_data_repository/files/001/dataset_1509.dat 0.57
# reading input file "/home/galaxy/Galaxy_data_repository/files/000/dataset_368.dat" of length 2403545
# matching query-file "/home/galaxy/Galaxy_data_repository/files/000/dataset_368.dat"
# against subject-file "/home/galaxy/Galaxy_data_repository/files/001/dataset_1509.dat"
# COMPLETETIME mummer /home/galaxy/Galaxy_data_repository/files/001/dataset_1509.dat 1.64
# SPACE mummer /home/galaxy/Galaxy_data_repository/files/001/dataset_1509.dat 4.66
defined(%hash) is deprecated at /home/galaxy/galaxy-dist/Tool_dependency/mummer/3.23/iuc/package_mummer_3_23/cc6c4d6ebceb/mummerplot line 884.
	(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /home/galaxy/galaxy-dist/Tool_dependency/mummer/3.23/iuc/package_mummer_3_23/cc6c4d6ebceb/mummerplot line 894.
	(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /home/galaxy/galaxy-dist/Tool_dependency/mummer/3.23/iuc/package_mummer_3_23/cc6c4d6ebceb/mummerplot line 981.
	(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /home/galaxy/galaxy-dist/Tool_dependency/mummer/3.23/iuc/package_mummer_3_23/cc6c4d6ebceb/mummerplot line 991.
	(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /home/galaxy/galaxy-dist/Tool_dependency/mummer/3.23/iuc/package_mummer_3_23/cc6c4d6ebceb/mummerplot line 1034.
	(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at /home/galaxy/galaxy-dist/Tool_dependency/mummer/3.23/iuc/package_mummer_3_23/cc6c4d6ebceb/mummerplot line 1044.
	(Maybe you should just omit the defined()?)
Reading mummer file /home/galaxy/galaxy-dist/database/tmp/tmpkA2dMi/ref_qry.mums (use mummer -c)
Writing plot files /home/galaxy/galaxy-dist/database/tmp/tmpkA2dMi/ref_qry.fplot, /home/galaxy/galaxy-dist/database/tmp/tmpkA2dMi/ref_qry.rplot
ERROR: No alignment data to plot
Error 6400 from: mummerplot -R "/home/galaxy/Galaxy_data_repository/files/001/dataset_1509.dat" -Q "/home/galaxy/Galaxy_data_repository/files/000/dataset_368.dat" --png --large --prefix=/home/galaxy/galaxy-dist/database/tmp/tmpkA2dMi/ref_qry /home/galaxy/galaxy-dist/database/tmp/tmpkA2dMi/ref_qry.mums

 

 

And when i am trying Nucmer it is working.

 

Any idea,

 

thanks a lot in advance,

 

 

error tool galaxy inputs • 1.1k views
ADD COMMENTlink modified 2.9 years ago by Jennifer Hillman Jackson23k • written 2.9 years ago by k.mamoud30
0
gravatar for Jennifer Hillman Jackson
2.9 years ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

This looks like an input format issue. Maybe go back and double check what the correct input format should be and then confirm against your dataset? This resolves a very large number of errors - small deviations from expected format can produce all sorts of odd errors.

Please give this a try, thanks, Jen, Galaxy team

ADD COMMENTlink written 2.9 years ago by Jennifer Hillman Jackson23k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 93 users visited in the last hour