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test mummerplot_wrapper/0.0.7 #91

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jennaj opened this issue Apr 14, 2023 · 8 comments
Open

test mummerplot_wrapper/0.0.7 #91

jennaj opened this issue Apr 14, 2023 · 8 comments

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@jennaj
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jennaj commented Apr 14, 2023

toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper/0.0.7
@jennaj
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jennaj commented Apr 14, 2023

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper/0.0.7

@mvdbeek
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mvdbeek commented Apr 14, 2023

Results (powered by Planemo)

Summary

State Count
Total 2
Passed 0
Error 0
Failure 2
Skipped 0
Failed s
  • ❌ toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper (Test tool test #1)

    Problems:

    • Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper/0.0.7, exit_code: 1, stderr: # reading input file "/corral4/main/objects/2/6/f/dataset_26fa801d-1167-43a9-8bc9-00bc3469fdf5.dat" of length 10734
# construct suffix tree for sequence of length 10734
# (maximum reference length is 2305843009213693948)
# (maximum query length is 18446744073709551615)
# CONSTRUCTIONTIME mummer /corral4/main/objects/2/6/f/dataset_26fa801d-1167-43a9-8bc9-00bc3469fdf5.dat 0.00
# reading input file "/corral4/main/objects/c/4/f/dataset_c4f29302-6d11-4ca8-aff9-af84b13bc7e5.dat" of length 10301
# matching query-file "/corral4/main/objects/c/4/f/dataset_c4f29302-6d11-4ca8-aff9-af84b13bc7e5.dat"
# against subject-file "/corral4/main/objects/2/6/f/dataset_26fa801d-1167-43a9-8bc9-00bc3469fdf5.dat"
# COMPLETETIME mummer /corral4/main/objects/2/6/f/dataset_26fa801d-1167-43a9-8bc9-00bc3469fdf5.dat 0.00
# SPACE mummer /corral4/main/objects/2/6/f/dataset_26fa801d-1167-43a9-8bc9-00bc3469fdf5.dat 0.02
Reading mummer file /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.mums (use mummer -c)
Writing plot files /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.fplot, /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.gp
Rendering plot /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.png

set terminal png tiny size 1400,1400
             ^
"/corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.gp", line 1: unknown or ambiguous terminal type; type just 'set terminal' for a list

WARNING: Unable to run 'gnuplot /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.gp', Inappropriate ioctl for device
Reading mummer file /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.mums (use mummer -c)
Writing plot files /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.fplot, /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.gp
Rendering plot /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.ps
Can't find PostScript prologue file prologue.ps
	loadpath is empty
	gnuplotrc is read from /anaconda/envs/_build/share/gnuplot/4.6
	no XAPPLRESDIR found in the environment,
	    falling back to "/etc/X11/app-defaults/"
Please copy prologue.ps to one of the above directories
or set the environmental variable GNUPLOT_PS_DIR
or set the loadpath appropriately
"/corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.gp", line 36: Plot failed!

WARNING: Unable to run 'gnuplot /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.gp', Inappropriate ioctl for device
ERROR: PNG file not created.
ERROR: Failed to produce output file(s).
.

    • Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper/0.0.7, exit_code: 1, stderr: # reading input file "/corral4/main/objects/2/6/f/dataset_26fa801d-1167-43a9-8bc9-00bc3469fdf5.dat" of length 10734
# construct suffix tree for sequence of length 10734
# (maximum reference length is 2305843009213693948)
# (maximum query length is 18446744073709551615)
# CONSTRUCTIONTIME mummer /corral4/main/objects/2/6/f/dataset_26fa801d-1167-43a9-8bc9-00bc3469fdf5.dat 0.00
# reading input file "/corral4/main/objects/c/4/f/dataset_c4f29302-6d11-4ca8-aff9-af84b13bc7e5.dat" of length 10301
# matching query-file "/corral4/main/objects/c/4/f/dataset_c4f29302-6d11-4ca8-aff9-af84b13bc7e5.dat"
# against subject-file "/corral4/main/objects/2/6/f/dataset_26fa801d-1167-43a9-8bc9-00bc3469fdf5.dat"
# COMPLETETIME mummer /corral4/main/objects/2/6/f/dataset_26fa801d-1167-43a9-8bc9-00bc3469fdf5.dat 0.00
# SPACE mummer /corral4/main/objects/2/6/f/dataset_26fa801d-1167-43a9-8bc9-00bc3469fdf5.dat 0.02
Reading mummer file /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.mums (use mummer -c)
Writing plot files /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.fplot, /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.gp
Rendering plot /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.png

set terminal png tiny size 1400,1400
             ^
"/corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.gp", line 1: unknown or ambiguous terminal type; type just 'set terminal' for a list

WARNING: Unable to run 'gnuplot /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.gp', Inappropriate ioctl for device
Reading mummer file /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.mums (use mummer -c)
Writing plot files /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.fplot, /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.gp
Rendering plot /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.ps
Can't find PostScript prologue file prologue.ps
	loadpath is empty
	gnuplotrc is read from /anaconda/envs/_build/share/gnuplot/4.6
	no XAPPLRESDIR found in the environment,
	    falling back to "/etc/X11/app-defaults/"
Please copy prologue.ps to one of the above directories
or set the environmental variable GNUPLOT_PS_DIR
or set the loadpath appropriately
"/corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.gp", line 36: Plot failed!

WARNING: Unable to run 'gnuplot /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.gp', Inappropriate ioctl for device
ERROR: PNG file not created.
ERROR: Failed to produce output file(s).
.

    • Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper/0.0.7, exit_code: 1, stderr: # reading input file "/corral4/main/objects/2/6/f/dataset_26fa801d-1167-43a9-8bc9-00bc3469fdf5.dat" of length 10734
# construct suffix tree for sequence of length 10734
# (maximum reference length is 2305843009213693948)
# (maximum query length is 18446744073709551615)
# CONSTRUCTIONTIME mummer /corral4/main/objects/2/6/f/dataset_26fa801d-1167-43a9-8bc9-00bc3469fdf5.dat 0.00
# reading input file "/corral4/main/objects/c/4/f/dataset_c4f29302-6d11-4ca8-aff9-af84b13bc7e5.dat" of length 10301
# matching query-file "/corral4/main/objects/c/4/f/dataset_c4f29302-6d11-4ca8-aff9-af84b13bc7e5.dat"
# against subject-file "/corral4/main/objects/2/6/f/dataset_26fa801d-1167-43a9-8bc9-00bc3469fdf5.dat"
# COMPLETETIME mummer /corral4/main/objects/2/6/f/dataset_26fa801d-1167-43a9-8bc9-00bc3469fdf5.dat 0.00
# SPACE mummer /corral4/main/objects/2/6/f/dataset_26fa801d-1167-43a9-8bc9-00bc3469fdf5.dat 0.02
Reading mummer file /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.mums (use mummer -c)
Writing plot files /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.fplot, /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.gp
Rendering plot /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.png

set terminal png tiny size 1400,1400
             ^
"/corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.gp", line 1: unknown or ambiguous terminal type; type just 'set terminal' for a list

WARNING: Unable to run 'gnuplot /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.gp', Inappropriate ioctl for device
Reading mummer file /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.mums (use mummer -c)
Writing plot files /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.fplot, /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.gp
Rendering plot /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.ps
Can't find PostScript prologue file prologue.ps
	loadpath is empty
	gnuplotrc is read from /anaconda/envs/_build/share/gnuplot/4.6
	no XAPPLRESDIR found in the environment,
	    falling back to "/etc/X11/app-defaults/"
Please copy prologue.ps to one of the above directories
or set the environmental variable GNUPLOT_PS_DIR
or set the loadpath appropriately
"/corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.gp", line 36: Plot failed!

WARNING: Unable to run 'gnuplot /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.gp', Inappropriate ioctl for device
ERROR: PNG file not created.
ERROR: Failed to produce output file(s).
.

    Command Line:

    • 

      • 

    

    Exit Code:
    

      

    • 

      1
      

      • 

    

    Standard Error:
    

      

    • 

      # reading input file "/corral4/main/objects/2/6/f/dataset_26fa801d-1167-43a9-8bc9-00bc3469fdf5.dat" of length 10734
# construct suffix tree for sequence of length 10734
# (maximum reference length is 2305843009213693948)
# (maximum query length is 18446744073709551615)
# CONSTRUCTIONTIME mummer /corral4/main/objects/2/6/f/dataset_26fa801d-1167-43a9-8bc9-00bc3469fdf5.dat 0.00
# reading input file "/corral4/main/objects/c/4/f/dataset_c4f29302-6d11-4ca8-aff9-af84b13bc7e5.dat" of length 10301
# matching query-file "/corral4/main/objects/c/4/f/dataset_c4f29302-6d11-4ca8-aff9-af84b13bc7e5.dat"
# against subject-file "/corral4/main/objects/2/6/f/dataset_26fa801d-1167-43a9-8bc9-00bc3469fdf5.dat"
# COMPLETETIME mummer /corral4/main/objects/2/6/f/dataset_26fa801d-1167-43a9-8bc9-00bc3469fdf5.dat 0.00
# SPACE mummer /corral4/main/objects/2/6/f/dataset_26fa801d-1167-43a9-8bc9-00bc3469fdf5.dat 0.02
Reading mummer file /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.mums (use mummer -c)
Writing plot files /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.fplot, /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.gp
Rendering plot /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.png

set terminal png tiny size 1400,1400
             ^
"/corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.gp", line 1: unknown or ambiguous terminal type; type just 'set terminal' for a list

WARNING: Unable to run 'gnuplot /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.gp', Inappropriate ioctl for device
Reading mummer file /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.mums (use mummer -c)
Writing plot files /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.fplot, /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.gp
Rendering plot /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.ps
Can't find PostScript prologue file prologue.ps
	loadpath is empty
	gnuplotrc is read from /anaconda/envs/_build/share/gnuplot/4.6
	no XAPPLRESDIR found in the environment,
	    falling back to "/etc/X11/app-defaults/"
Please copy prologue.ps to one of the above directories
or set the environmental variable GNUPLOT_PS_DIR
or set the loadpath appropriately
"/corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.gp", line 36: Plot failed!

WARNING: Unable to run 'gnuplot /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.gp', Inappropriate ioctl for device
ERROR: PNG file not created.
ERROR: Failed to produce output file(s).

      

      • 

    

    Standard Output:
    

      

    • 

      gnuplot 4.6 patchlevel 0
gnuplot 4.6 patchlevel 0
mummer -mum -b -c "/corral4/main/objects/2/6/f/dataset_26fa801d-1167-43a9-8bc9-00bc3469fdf5.dat" "/corral4/main/objects/c/4/f/dataset_c4f29302-6d11-4ca8-aff9-af84b13bc7e5.dat" > /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.mums
mummerplot -R "/corral4/main/objects/2/6/f/dataset_26fa801d-1167-43a9-8bc9-00bc3469fdf5.dat" -Q "/corral4/main/objects/c/4/f/dataset_c4f29302-6d11-4ca8-aff9-af84b13bc7e5.dat" --png --large --prefix=/corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.mums
mummerplot -R "/corral4/main/objects/2/6/f/dataset_26fa801d-1167-43a9-8bc9-00bc3469fdf5.dat" -Q "/corral4/main/objects/c/4/f/dataset_c4f29302-6d11-4ca8-aff9-af84b13bc7e5.dat" --postscript --small --prefix=/corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.mums
ps2pdf -dEPSCrop "/corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.ps" "/corral4/main/objects/e/0/4/dataset_e04c3c3a-c684-4806-b6bd-eff7553e29cd.dat"

      

      • 

    

    Traceback:
    

      

    • 

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
algorithm
"mummer"

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"fasta"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper (Test test against test.galaxyproject.org #2)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper/0.0.7, exit_code: 1, stderr: 1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "out.ntref" of length 10735
# construct suffix tree for sequence of length 10735
# (maximum reference length is 2305843009213693948)
# (maximum query length is 18446744073709551615)
# CONSTRUCTIONTIME /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.00
# reading input file "/corral4/main/objects/c/4/f/dataset_c4f29302-6d11-4ca8-aff9-af84b13bc7e5.dat" of length 10301
# matching query-file "/corral4/main/objects/c/4/f/dataset_c4f29302-6d11-4ca8-aff9-af84b13bc7e5.dat"
# against subject-file "out.ntref"
# COMPLETETIME /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.00
# SPACE /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.02
4: FINISHING DATA
Reading delta file out.delta
Writing plot files /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.fplot, /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.gp
Rendering plot /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.png

set terminal png tiny size 1400,1400
             ^
"/corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.gp", line 1: unknown or ambiguous terminal type; type just 'set terminal' for a list

WARNING: Unable to run 'gnuplot /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.gp', Inappropriate ioctl for device
Reading delta file out.delta
Writing plot files /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.fplot, /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.gp
Rendering plot /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.ps
Can't find PostScript prologue file prologue.ps
	loadpath is empty
	gnuplotrc is read from /anaconda/envs/_build/share/gnuplot/4.6
	no XAPPLRESDIR found in the environment,
	    falling back to "/etc/X11/app-defaults/"
Please copy prologue.ps to one of the above directories
or set the environmental variable GNUPLOT_PS_DIR
or set the loadpath appropriately
"/corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.gp", line 36: Plot failed!

WARNING: Unable to run 'gnuplot /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.gp', Inappropriate ioctl for device
ERROR: PNG file not created.
ERROR: Failed to produce output file(s).
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper/0.0.7, exit_code: 1, stderr: 1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "out.ntref" of length 10735
# construct suffix tree for sequence of length 10735
# (maximum reference length is 2305843009213693948)
# (maximum query length is 18446744073709551615)
# CONSTRUCTIONTIME /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.00
# reading input file "/corral4/main/objects/c/4/f/dataset_c4f29302-6d11-4ca8-aff9-af84b13bc7e5.dat" of length 10301
# matching query-file "/corral4/main/objects/c/4/f/dataset_c4f29302-6d11-4ca8-aff9-af84b13bc7e5.dat"
# against subject-file "out.ntref"
# COMPLETETIME /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.00
# SPACE /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.02
4: FINISHING DATA
Reading delta file out.delta
Writing plot files /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.fplot, /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.gp
Rendering plot /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.png

set terminal png tiny size 1400,1400
             ^
"/corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.gp", line 1: unknown or ambiguous terminal type; type just 'set terminal' for a list

WARNING: Unable to run 'gnuplot /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.gp', Inappropriate ioctl for device
Reading delta file out.delta
Writing plot files /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.fplot, /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.gp
Rendering plot /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.ps
Can't find PostScript prologue file prologue.ps
	loadpath is empty
	gnuplotrc is read from /anaconda/envs/_build/share/gnuplot/4.6
	no XAPPLRESDIR found in the environment,
	    falling back to "/etc/X11/app-defaults/"
Please copy prologue.ps to one of the above directories
or set the environmental variable GNUPLOT_PS_DIR
or set the loadpath appropriately
"/corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.gp", line 36: Plot failed!

WARNING: Unable to run 'gnuplot /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.gp', Inappropriate ioctl for device
ERROR: PNG file not created.
ERROR: Failed to produce output file(s).
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper/0.0.7, exit_code: 1, stderr: 1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "out.ntref" of length 10735
# construct suffix tree for sequence of length 10735
# (maximum reference length is 2305843009213693948)
# (maximum query length is 18446744073709551615)
# CONSTRUCTIONTIME /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.00
# reading input file "/corral4/main/objects/c/4/f/dataset_c4f29302-6d11-4ca8-aff9-af84b13bc7e5.dat" of length 10301
# matching query-file "/corral4/main/objects/c/4/f/dataset_c4f29302-6d11-4ca8-aff9-af84b13bc7e5.dat"
# against subject-file "out.ntref"
# COMPLETETIME /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.00
# SPACE /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.02
4: FINISHING DATA
Reading delta file out.delta
Writing plot files /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.fplot, /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.gp
Rendering plot /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.png

set terminal png tiny size 1400,1400
             ^
"/corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.gp", line 1: unknown or ambiguous terminal type; type just 'set terminal' for a list

WARNING: Unable to run 'gnuplot /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.gp', Inappropriate ioctl for device
Reading delta file out.delta
Writing plot files /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.fplot, /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.gp
Rendering plot /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.ps
Can't find PostScript prologue file prologue.ps
	loadpath is empty
	gnuplotrc is read from /anaconda/envs/_build/share/gnuplot/4.6
	no XAPPLRESDIR found in the environment,
	    falling back to "/etc/X11/app-defaults/"
Please copy prologue.ps to one of the above directories
or set the environmental variable GNUPLOT_PS_DIR
or set the loadpath appropriately
"/corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.gp", line 36: Plot failed!

WARNING: Unable to run 'gnuplot /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.gp', Inappropriate ioctl for device
ERROR: PNG file not created.
ERROR: Failed to produce output file(s).
.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      1
      

      • 

    

    Standard Error:
    

      

    • 

      1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "out.ntref" of length 10735
# construct suffix tree for sequence of length 10735
# (maximum reference length is 2305843009213693948)
# (maximum query length is 18446744073709551615)
# CONSTRUCTIONTIME /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.00
# reading input file "/corral4/main/objects/c/4/f/dataset_c4f29302-6d11-4ca8-aff9-af84b13bc7e5.dat" of length 10301
# matching query-file "/corral4/main/objects/c/4/f/dataset_c4f29302-6d11-4ca8-aff9-af84b13bc7e5.dat"
# against subject-file "out.ntref"
# COMPLETETIME /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.00
# SPACE /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.02
4: FINISHING DATA
Reading delta file out.delta
Writing plot files /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.fplot, /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.gp
Rendering plot /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.png

set terminal png tiny size 1400,1400
             ^
"/corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.gp", line 1: unknown or ambiguous terminal type; type just 'set terminal' for a list

WARNING: Unable to run 'gnuplot /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.gp', Inappropriate ioctl for device
Reading delta file out.delta
Writing plot files /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.fplot, /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.gp
Rendering plot /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.ps
Can't find PostScript prologue file prologue.ps
	loadpath is empty
	gnuplotrc is read from /anaconda/envs/_build/share/gnuplot/4.6
	no XAPPLRESDIR found in the environment,
	    falling back to "/etc/X11/app-defaults/"
Please copy prologue.ps to one of the above directories
or set the environmental variable GNUPLOT_PS_DIR
or set the loadpath appropriately
"/corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.gp", line 36: Plot failed!

WARNING: Unable to run 'gnuplot /corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.gp', Inappropriate ioctl for device
ERROR: PNG file not created.
ERROR: Failed to produce output file(s).

      

      • 

    

    Standard Output:
    

      

    • 

      gnuplot 4.6 patchlevel 0
gnuplot 4.6 patchlevel 0
nucmer "/corral4/main/objects/2/6/f/dataset_26fa801d-1167-43a9-8bc9-00bc3469fdf5.dat" "/corral4/main/objects/c/4/f/dataset_c4f29302-6d11-4ca8-aff9-af84b13bc7e5.dat"
mummerplot -R "/corral4/main/objects/2/6/f/dataset_26fa801d-1167-43a9-8bc9-00bc3469fdf5.dat" -Q "/corral4/main/objects/c/4/f/dataset_c4f29302-6d11-4ca8-aff9-af84b13bc7e5.dat" --png --large --prefix=/corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry out.delta
mummerplot -R "/corral4/main/objects/2/6/f/dataset_26fa801d-1167-43a9-8bc9-00bc3469fdf5.dat" -Q "/corral4/main/objects/c/4/f/dataset_c4f29302-6d11-4ca8-aff9-af84b13bc7e5.dat" --postscript --small --prefix=/corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry out.delta
ps2pdf -dEPSCrop "/corral4/main/jobs/049/522/49522533/_job_tmp/tmpttm8i2pm/ref_qry.ps" "/corral4/main/objects/4/1/c/dataset_41c78d9c-1caf-44a7-8eb8-acc92690f79b.dat"

      

      • 

    

    Traceback:
    

      

    • 

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
algorithm
"nucmer"

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"fasta"

      
      

      

      • 

    

    

    • 




      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @jennaj





  


    

      

  

    

        
    
    

  


      
          
  
      
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            jennaj
  

      

      

      commented


        Apr 14, 2023


      
    


  





      


        


  
    

      
          
Looks similar to this mummer4/mummer#36

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
          

  

    
  


  

      

    @jennaj
jennaj



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      Apr 14, 2023
    





  


  

      
  
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  @jennaj





  


    

      

  

    

        
    
    

  


      
          
  
      
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            jennaj
  

      

      

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        Jun 12, 2023


      
    


  





      


        


  
    

      
          
/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper/0.0.7

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @mvdbeek





  


    

      

  

    

        
    
    

  


      
          
  
      
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            mvdbeek
  

      

      

      commented


        Jun 12, 2023


      
    


  





      


        


  
    

      
          
Results (powered by Planemo)


Summary



  

  

  

  

  

  








State
Count






Total
2




Passed
0




Error
0




Failure
2




Skipped
0






Failed s

    

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper (Test tool test #1)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper/0.0.7, exit_code: 1, stderr: # reading input file "/corral4/main/objects/9/a/b/dataset_9abc447a-059c-4be6-a0ed-d6c9bf8a3493.dat" of length 10734
# construct suffix tree for sequence of length 10734
# (maximum reference length is 2305843009213693948)
# (maximum query length is 18446744073709551615)
# CONSTRUCTIONTIME mummer /corral4/main/objects/9/a/b/dataset_9abc447a-059c-4be6-a0ed-d6c9bf8a3493.dat 0.00
# reading input file "/corral4/main/objects/c/c/1/dataset_cc1811d9-7706-4dcf-8325-d3981dd20968.dat" of length 10301
# matching query-file "/corral4/main/objects/c/c/1/dataset_cc1811d9-7706-4dcf-8325-d3981dd20968.dat"
# against subject-file "/corral4/main/objects/9/a/b/dataset_9abc447a-059c-4be6-a0ed-d6c9bf8a3493.dat"
# COMPLETETIME mummer /corral4/main/objects/9/a/b/dataset_9abc447a-059c-4be6-a0ed-d6c9bf8a3493.dat 0.00
# SPACE mummer /corral4/main/objects/9/a/b/dataset_9abc447a-059c-4be6-a0ed-d6c9bf8a3493.dat 0.02
Reading mummer file /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.mums (use mummer -c)
Writing plot files /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.fplot, /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.gp
Rendering plot /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.png

set terminal png tiny size 1400,1400
             ^
"/corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.gp", line 1: unknown or ambiguous terminal type; type just 'set terminal' for a list

WARNING: Unable to run 'gnuplot /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.gp', Inappropriate ioctl for device
Reading mummer file /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.mums (use mummer -c)
Writing plot files /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.fplot, /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.gp
Rendering plot /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.ps
Can't find PostScript prologue file prologue.ps
	loadpath is empty
	gnuplotrc is read from /anaconda/envs/_build/share/gnuplot/4.6
	no XAPPLRESDIR found in the environment,
	    falling back to "/etc/X11/app-defaults/"
Please copy prologue.ps to one of the above directories
or set the environmental variable GNUPLOT_PS_DIR
or set the loadpath appropriately
"/corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.gp", line 36: Plot failed!

WARNING: Unable to run 'gnuplot /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.gp', Inappropriate ioctl for device
ERROR: PNG file not created.
ERROR: Failed to produce output file(s).
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper/0.0.7, exit_code: 1, stderr: # reading input file "/corral4/main/objects/9/a/b/dataset_9abc447a-059c-4be6-a0ed-d6c9bf8a3493.dat" of length 10734
# construct suffix tree for sequence of length 10734
# (maximum reference length is 2305843009213693948)
# (maximum query length is 18446744073709551615)
# CONSTRUCTIONTIME mummer /corral4/main/objects/9/a/b/dataset_9abc447a-059c-4be6-a0ed-d6c9bf8a3493.dat 0.00
# reading input file "/corral4/main/objects/c/c/1/dataset_cc1811d9-7706-4dcf-8325-d3981dd20968.dat" of length 10301
# matching query-file "/corral4/main/objects/c/c/1/dataset_cc1811d9-7706-4dcf-8325-d3981dd20968.dat"
# against subject-file "/corral4/main/objects/9/a/b/dataset_9abc447a-059c-4be6-a0ed-d6c9bf8a3493.dat"
# COMPLETETIME mummer /corral4/main/objects/9/a/b/dataset_9abc447a-059c-4be6-a0ed-d6c9bf8a3493.dat 0.00
# SPACE mummer /corral4/main/objects/9/a/b/dataset_9abc447a-059c-4be6-a0ed-d6c9bf8a3493.dat 0.02
Reading mummer file /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.mums (use mummer -c)
Writing plot files /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.fplot, /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.gp
Rendering plot /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.png

set terminal png tiny size 1400,1400
             ^
"/corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.gp", line 1: unknown or ambiguous terminal type; type just 'set terminal' for a list

WARNING: Unable to run 'gnuplot /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.gp', Inappropriate ioctl for device
Reading mummer file /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.mums (use mummer -c)
Writing plot files /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.fplot, /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.gp
Rendering plot /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.ps
Can't find PostScript prologue file prologue.ps
	loadpath is empty
	gnuplotrc is read from /anaconda/envs/_build/share/gnuplot/4.6
	no XAPPLRESDIR found in the environment,
	    falling back to "/etc/X11/app-defaults/"
Please copy prologue.ps to one of the above directories
or set the environmental variable GNUPLOT_PS_DIR
or set the loadpath appropriately
"/corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.gp", line 36: Plot failed!

WARNING: Unable to run 'gnuplot /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.gp', Inappropriate ioctl for device
ERROR: PNG file not created.
ERROR: Failed to produce output file(s).
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper/0.0.7, exit_code: 1, stderr: # reading input file "/corral4/main/objects/9/a/b/dataset_9abc447a-059c-4be6-a0ed-d6c9bf8a3493.dat" of length 10734
# construct suffix tree for sequence of length 10734
# (maximum reference length is 2305843009213693948)
# (maximum query length is 18446744073709551615)
# CONSTRUCTIONTIME mummer /corral4/main/objects/9/a/b/dataset_9abc447a-059c-4be6-a0ed-d6c9bf8a3493.dat 0.00
# reading input file "/corral4/main/objects/c/c/1/dataset_cc1811d9-7706-4dcf-8325-d3981dd20968.dat" of length 10301
# matching query-file "/corral4/main/objects/c/c/1/dataset_cc1811d9-7706-4dcf-8325-d3981dd20968.dat"
# against subject-file "/corral4/main/objects/9/a/b/dataset_9abc447a-059c-4be6-a0ed-d6c9bf8a3493.dat"
# COMPLETETIME mummer /corral4/main/objects/9/a/b/dataset_9abc447a-059c-4be6-a0ed-d6c9bf8a3493.dat 0.00
# SPACE mummer /corral4/main/objects/9/a/b/dataset_9abc447a-059c-4be6-a0ed-d6c9bf8a3493.dat 0.02
Reading mummer file /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.mums (use mummer -c)
Writing plot files /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.fplot, /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.gp
Rendering plot /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.png

set terminal png tiny size 1400,1400
             ^
"/corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.gp", line 1: unknown or ambiguous terminal type; type just 'set terminal' for a list

WARNING: Unable to run 'gnuplot /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.gp', Inappropriate ioctl for device
Reading mummer file /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.mums (use mummer -c)
Writing plot files /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.fplot, /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.gp
Rendering plot /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.ps
Can't find PostScript prologue file prologue.ps
	loadpath is empty
	gnuplotrc is read from /anaconda/envs/_build/share/gnuplot/4.6
	no XAPPLRESDIR found in the environment,
	    falling back to "/etc/X11/app-defaults/"
Please copy prologue.ps to one of the above directories
or set the environmental variable GNUPLOT_PS_DIR
or set the loadpath appropriately
"/corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.gp", line 36: Plot failed!

WARNING: Unable to run 'gnuplot /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.gp', Inappropriate ioctl for device
ERROR: PNG file not created.
ERROR: Failed to produce output file(s).
.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      1
      

      • 

    

    Standard Error:
    

      

    • 

      # reading input file "/corral4/main/objects/9/a/b/dataset_9abc447a-059c-4be6-a0ed-d6c9bf8a3493.dat" of length 10734
# construct suffix tree for sequence of length 10734
# (maximum reference length is 2305843009213693948)
# (maximum query length is 18446744073709551615)
# CONSTRUCTIONTIME mummer /corral4/main/objects/9/a/b/dataset_9abc447a-059c-4be6-a0ed-d6c9bf8a3493.dat 0.00
# reading input file "/corral4/main/objects/c/c/1/dataset_cc1811d9-7706-4dcf-8325-d3981dd20968.dat" of length 10301
# matching query-file "/corral4/main/objects/c/c/1/dataset_cc1811d9-7706-4dcf-8325-d3981dd20968.dat"
# against subject-file "/corral4/main/objects/9/a/b/dataset_9abc447a-059c-4be6-a0ed-d6c9bf8a3493.dat"
# COMPLETETIME mummer /corral4/main/objects/9/a/b/dataset_9abc447a-059c-4be6-a0ed-d6c9bf8a3493.dat 0.00
# SPACE mummer /corral4/main/objects/9/a/b/dataset_9abc447a-059c-4be6-a0ed-d6c9bf8a3493.dat 0.02
Reading mummer file /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.mums (use mummer -c)
Writing plot files /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.fplot, /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.gp
Rendering plot /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.png

set terminal png tiny size 1400,1400
             ^
"/corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.gp", line 1: unknown or ambiguous terminal type; type just 'set terminal' for a list

WARNING: Unable to run 'gnuplot /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.gp', Inappropriate ioctl for device
Reading mummer file /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.mums (use mummer -c)
Writing plot files /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.fplot, /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.gp
Rendering plot /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.ps
Can't find PostScript prologue file prologue.ps
	loadpath is empty
	gnuplotrc is read from /anaconda/envs/_build/share/gnuplot/4.6
	no XAPPLRESDIR found in the environment,
	    falling back to "/etc/X11/app-defaults/"
Please copy prologue.ps to one of the above directories
or set the environmental variable GNUPLOT_PS_DIR
or set the loadpath appropriately
"/corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.gp", line 36: Plot failed!

WARNING: Unable to run 'gnuplot /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.gp', Inappropriate ioctl for device
ERROR: PNG file not created.
ERROR: Failed to produce output file(s).

      

      • 

    

    Standard Output:
    

      

    • 

      gnuplot 4.6 patchlevel 0
gnuplot 4.6 patchlevel 0
mummer -mum -b -c "/corral4/main/objects/9/a/b/dataset_9abc447a-059c-4be6-a0ed-d6c9bf8a3493.dat" "/corral4/main/objects/c/c/1/dataset_cc1811d9-7706-4dcf-8325-d3981dd20968.dat" > /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.mums
mummerplot -R "/corral4/main/objects/9/a/b/dataset_9abc447a-059c-4be6-a0ed-d6c9bf8a3493.dat" -Q "/corral4/main/objects/c/c/1/dataset_cc1811d9-7706-4dcf-8325-d3981dd20968.dat" --png --large --prefix=/corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.mums
mummerplot -R "/corral4/main/objects/9/a/b/dataset_9abc447a-059c-4be6-a0ed-d6c9bf8a3493.dat" -Q "/corral4/main/objects/c/c/1/dataset_cc1811d9-7706-4dcf-8325-d3981dd20968.dat" --postscript --small --prefix=/corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.mums
ps2pdf -dEPSCrop "/corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.ps" "/corral4/main/objects/1/0/1/dataset_101e02b0-bfec-4a04-818c-67ca1fb39348.dat"

      

      • 

    

    Traceback:
    

      

    • 

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
algorithm
"mummer"

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"fasta"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper (Test test against test.galaxyproject.org #2)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper/0.0.7, exit_code: 1, stderr: 1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "out.ntref" of length 10735
# construct suffix tree for sequence of length 10735
# (maximum reference length is 2305843009213693948)
# (maximum query length is 18446744073709551615)
# CONSTRUCTIONTIME /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.00
# reading input file "/corral4/main/objects/c/c/1/dataset_cc1811d9-7706-4dcf-8325-d3981dd20968.dat" of length 10301
# matching query-file "/corral4/main/objects/c/c/1/dataset_cc1811d9-7706-4dcf-8325-d3981dd20968.dat"
# against subject-file "out.ntref"
# COMPLETETIME /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.00
# SPACE /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.02
4: FINISHING DATA
Reading delta file out.delta
Writing plot files /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.fplot, /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.gp
Rendering plot /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.png

set terminal png tiny size 1400,1400
             ^
"/corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.gp", line 1: unknown or ambiguous terminal type; type just 'set terminal' for a list

WARNING: Unable to run 'gnuplot /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.gp', Inappropriate ioctl for device
Reading delta file out.delta
Writing plot files /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.fplot, /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.gp
Rendering plot /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.ps
Can't find PostScript prologue file prologue.ps
	loadpath is empty
	gnuplotrc is read from /anaconda/envs/_build/share/gnuplot/4.6
	no XAPPLRESDIR found in the environment,
	    falling back to "/etc/X11/app-defaults/"
Please copy prologue.ps to one of the above directories
or set the environmental variable GNUPLOT_PS_DIR
or set the loadpath appropriately
"/corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.gp", line 36: Plot failed!

WARNING: Unable to run 'gnuplot /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.gp', Inappropriate ioctl for device
ERROR: PNG file not created.
ERROR: Failed to produce output file(s).
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper/0.0.7, exit_code: 1, stderr: 1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "out.ntref" of length 10735
# construct suffix tree for sequence of length 10735
# (maximum reference length is 2305843009213693948)
# (maximum query length is 18446744073709551615)
# CONSTRUCTIONTIME /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.00
# reading input file "/corral4/main/objects/c/c/1/dataset_cc1811d9-7706-4dcf-8325-d3981dd20968.dat" of length 10301
# matching query-file "/corral4/main/objects/c/c/1/dataset_cc1811d9-7706-4dcf-8325-d3981dd20968.dat"
# against subject-file "out.ntref"
# COMPLETETIME /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.00
# SPACE /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.02
4: FINISHING DATA
Reading delta file out.delta
Writing plot files /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.fplot, /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.gp
Rendering plot /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.png

set terminal png tiny size 1400,1400
             ^
"/corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.gp", line 1: unknown or ambiguous terminal type; type just 'set terminal' for a list

WARNING: Unable to run 'gnuplot /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.gp', Inappropriate ioctl for device
Reading delta file out.delta
Writing plot files /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.fplot, /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.gp
Rendering plot /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.ps
Can't find PostScript prologue file prologue.ps
	loadpath is empty
	gnuplotrc is read from /anaconda/envs/_build/share/gnuplot/4.6
	no XAPPLRESDIR found in the environment,
	    falling back to "/etc/X11/app-defaults/"
Please copy prologue.ps to one of the above directories
or set the environmental variable GNUPLOT_PS_DIR
or set the loadpath appropriately
"/corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.gp", line 36: Plot failed!

WARNING: Unable to run 'gnuplot /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.gp', Inappropriate ioctl for device
ERROR: PNG file not created.
ERROR: Failed to produce output file(s).
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper/0.0.7, exit_code: 1, stderr: 1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "out.ntref" of length 10735
# construct suffix tree for sequence of length 10735
# (maximum reference length is 2305843009213693948)
# (maximum query length is 18446744073709551615)
# CONSTRUCTIONTIME /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.00
# reading input file "/corral4/main/objects/c/c/1/dataset_cc1811d9-7706-4dcf-8325-d3981dd20968.dat" of length 10301
# matching query-file "/corral4/main/objects/c/c/1/dataset_cc1811d9-7706-4dcf-8325-d3981dd20968.dat"
# against subject-file "out.ntref"
# COMPLETETIME /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.00
# SPACE /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.02
4: FINISHING DATA
Reading delta file out.delta
Writing plot files /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.fplot, /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.gp
Rendering plot /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.png

set terminal png tiny size 1400,1400
             ^
"/corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.gp", line 1: unknown or ambiguous terminal type; type just 'set terminal' for a list

WARNING: Unable to run 'gnuplot /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.gp', Inappropriate ioctl for device
Reading delta file out.delta
Writing plot files /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.fplot, /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.gp
Rendering plot /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.ps
Can't find PostScript prologue file prologue.ps
	loadpath is empty
	gnuplotrc is read from /anaconda/envs/_build/share/gnuplot/4.6
	no XAPPLRESDIR found in the environment,
	    falling back to "/etc/X11/app-defaults/"
Please copy prologue.ps to one of the above directories
or set the environmental variable GNUPLOT_PS_DIR
or set the loadpath appropriately
"/corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.gp", line 36: Plot failed!

WARNING: Unable to run 'gnuplot /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.gp', Inappropriate ioctl for device
ERROR: PNG file not created.
ERROR: Failed to produce output file(s).
.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      1
      

      • 

    

    Standard Error:
    

      

    • 

      1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "out.ntref" of length 10735
# construct suffix tree for sequence of length 10735
# (maximum reference length is 2305843009213693948)
# (maximum query length is 18446744073709551615)
# CONSTRUCTIONTIME /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.00
# reading input file "/corral4/main/objects/c/c/1/dataset_cc1811d9-7706-4dcf-8325-d3981dd20968.dat" of length 10301
# matching query-file "/corral4/main/objects/c/c/1/dataset_cc1811d9-7706-4dcf-8325-d3981dd20968.dat"
# against subject-file "out.ntref"
# COMPLETETIME /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.00
# SPACE /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.02
4: FINISHING DATA
Reading delta file out.delta
Writing plot files /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.fplot, /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.gp
Rendering plot /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.png

set terminal png tiny size 1400,1400
             ^
"/corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.gp", line 1: unknown or ambiguous terminal type; type just 'set terminal' for a list

WARNING: Unable to run 'gnuplot /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.gp', Inappropriate ioctl for device
Reading delta file out.delta
Writing plot files /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.fplot, /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.gp
Rendering plot /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.ps
Can't find PostScript prologue file prologue.ps
	loadpath is empty
	gnuplotrc is read from /anaconda/envs/_build/share/gnuplot/4.6
	no XAPPLRESDIR found in the environment,
	    falling back to "/etc/X11/app-defaults/"
Please copy prologue.ps to one of the above directories
or set the environmental variable GNUPLOT_PS_DIR
or set the loadpath appropriately
"/corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.gp", line 36: Plot failed!

WARNING: Unable to run 'gnuplot /corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.gp', Inappropriate ioctl for device
ERROR: PNG file not created.
ERROR: Failed to produce output file(s).

      

      • 

    

    Standard Output:
    

      

    • 

      gnuplot 4.6 patchlevel 0
gnuplot 4.6 patchlevel 0
nucmer "/corral4/main/objects/9/a/b/dataset_9abc447a-059c-4be6-a0ed-d6c9bf8a3493.dat" "/corral4/main/objects/c/c/1/dataset_cc1811d9-7706-4dcf-8325-d3981dd20968.dat"
mummerplot -R "/corral4/main/objects/9/a/b/dataset_9abc447a-059c-4be6-a0ed-d6c9bf8a3493.dat" -Q "/corral4/main/objects/c/c/1/dataset_cc1811d9-7706-4dcf-8325-d3981dd20968.dat" --png --large --prefix=/corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry out.delta
mummerplot -R "/corral4/main/objects/9/a/b/dataset_9abc447a-059c-4be6-a0ed-d6c9bf8a3493.dat" -Q "/corral4/main/objects/c/c/1/dataset_cc1811d9-7706-4dcf-8325-d3981dd20968.dat" --postscript --small --prefix=/corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry out.delta
ps2pdf -dEPSCrop "/corral4/main/jobs/050/972/50972784/_job_tmp/tmp6x81hfee/ref_qry.ps" "/corral4/main/objects/b/9/9/dataset_b99c23cf-f0d9-4d23-a832-20e5d36867bc.dat"

      

      • 

    

    Traceback:
    

      

    • 

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
algorithm
"nucmer"

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"fasta"

      
      

      

      • 

    

    

    • 




      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @jennaj





  


    

      

  

    

        
    
    

  


      
          
  
      
            Copy link

  

      
    

  


  

      

  
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  Author


  


  

    

      

      
            jennaj
  

      

      

      commented


        Jun 17, 2023


      
    


  





      


        


  
    

      
          
Dependency problem. Trying one more rerun




Rendering plot /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.png


set terminal png tiny size 1400,1400

^

"/corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.gp", line 1: unknown or ambiguous terminal type; type just 'set terminal' for a list


WARNING: Unable to run 'gnuplot /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.gp', Inappropriate ioctl for device

Reading mummer file /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.mums (use mummer -c)

Writing plot files /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.fplot, /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.rplot

Writing gnuplot script /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.gp

Rendering plot /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.ps

Can't find PostScript prologue file prologue.ps

loadpath is empty

gnuplotrc is read from /anaconda/envs/_build/share/gnuplot/4.6

no XAPPLRESDIR found in the environment,

falling back to "/etc/X11/app-defaults/"

Please copy prologue.ps to one of the above directories

or set the environmental variable GNUPLOT_PS_DIR

or set the loadpath appropriately

"/corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.gp", line 36: Plot failed!


WARNING: Unable to run 'gnuplot /corral4/main/jobs/050/972/50972785/_job_tmp/tmppyn7vcwo/ref_qry.gp', Inappropriate ioctl for device

ERROR: PNG file not created.

ERROR: Failed to produce output file(s).



      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @jennaj





  


    

      

  

    

        
    
    

  


      
          
  
      
            Copy link

  

      
    

  


  

      

  
    Collaborator


      

  Author


  


  

    

      

      
            jennaj
  

      

      

      commented


        Jun 17, 2023


      
    


  





      


        


  
    

      
          
/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper/0.0.7

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @mvdbeek





  


    

      

  

    

        
    
    

  


      
          
  
      
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            mvdbeek
  

      

      

      commented


        Jun 17, 2023


      
    


  





      


        


  
    

      
          
Results (powered by Planemo)


Summary



  

  

  

  

  

  








State
Count






Total
2




Passed
0




Error
0




Failure
2




Skipped
0






Failed s

    

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper (Test tool test #1)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper/0.0.7, exit_code: 1, stderr: # reading input file "/corral4/main/objects/e/c/5/dataset_ec5ecef7-71ad-4071-b401-017f2ee5e2f8.dat" of length 10734
# construct suffix tree for sequence of length 10734
# (maximum reference length is 2305843009213693948)
# (maximum query length is 18446744073709551615)
# CONSTRUCTIONTIME mummer /corral4/main/objects/e/c/5/dataset_ec5ecef7-71ad-4071-b401-017f2ee5e2f8.dat 0.00
# reading input file "/corral4/main/objects/3/9/c/dataset_39c49fdf-3801-4bd7-989b-efccf3a2760f.dat" of length 10301
# matching query-file "/corral4/main/objects/3/9/c/dataset_39c49fdf-3801-4bd7-989b-efccf3a2760f.dat"
# against subject-file "/corral4/main/objects/e/c/5/dataset_ec5ecef7-71ad-4071-b401-017f2ee5e2f8.dat"
# COMPLETETIME mummer /corral4/main/objects/e/c/5/dataset_ec5ecef7-71ad-4071-b401-017f2ee5e2f8.dat 0.00
# SPACE mummer /corral4/main/objects/e/c/5/dataset_ec5ecef7-71ad-4071-b401-017f2ee5e2f8.dat 0.02
Reading mummer file /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.mums (use mummer -c)
Writing plot files /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.fplot, /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.gp
Rendering plot /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.png

set terminal png tiny size 1400,1400
             ^
"/corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.gp", line 1: unknown or ambiguous terminal type; type just 'set terminal' for a list

WARNING: Unable to run 'gnuplot /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.gp', Inappropriate ioctl for device
Reading mummer file /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.mums (use mummer -c)
Writing plot files /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.fplot, /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.gp
Rendering plot /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.ps
Can't find PostScript prologue file prologue.ps
	loadpath is empty
	gnuplotrc is read from /anaconda/envs/_build/share/gnuplot/4.6
	no XAPPLRESDIR found in the environment,
	    falling back to "/etc/X11/app-defaults/"
Please copy prologue.ps to one of the above directories
or set the environmental variable GNUPLOT_PS_DIR
or set the loadpath appropriately
"/corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.gp", line 36: Plot failed!

WARNING: Unable to run 'gnuplot /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.gp', Inappropriate ioctl for device
ERROR: PNG file not created.
ERROR: Failed to produce output file(s).
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper/0.0.7, exit_code: 1, stderr: # reading input file "/corral4/main/objects/e/c/5/dataset_ec5ecef7-71ad-4071-b401-017f2ee5e2f8.dat" of length 10734
# construct suffix tree for sequence of length 10734
# (maximum reference length is 2305843009213693948)
# (maximum query length is 18446744073709551615)
# CONSTRUCTIONTIME mummer /corral4/main/objects/e/c/5/dataset_ec5ecef7-71ad-4071-b401-017f2ee5e2f8.dat 0.00
# reading input file "/corral4/main/objects/3/9/c/dataset_39c49fdf-3801-4bd7-989b-efccf3a2760f.dat" of length 10301
# matching query-file "/corral4/main/objects/3/9/c/dataset_39c49fdf-3801-4bd7-989b-efccf3a2760f.dat"
# against subject-file "/corral4/main/objects/e/c/5/dataset_ec5ecef7-71ad-4071-b401-017f2ee5e2f8.dat"
# COMPLETETIME mummer /corral4/main/objects/e/c/5/dataset_ec5ecef7-71ad-4071-b401-017f2ee5e2f8.dat 0.00
# SPACE mummer /corral4/main/objects/e/c/5/dataset_ec5ecef7-71ad-4071-b401-017f2ee5e2f8.dat 0.02
Reading mummer file /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.mums (use mummer -c)
Writing plot files /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.fplot, /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.gp
Rendering plot /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.png

set terminal png tiny size 1400,1400
             ^
"/corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.gp", line 1: unknown or ambiguous terminal type; type just 'set terminal' for a list

WARNING: Unable to run 'gnuplot /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.gp', Inappropriate ioctl for device
Reading mummer file /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.mums (use mummer -c)
Writing plot files /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.fplot, /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.gp
Rendering plot /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.ps
Can't find PostScript prologue file prologue.ps
	loadpath is empty
	gnuplotrc is read from /anaconda/envs/_build/share/gnuplot/4.6
	no XAPPLRESDIR found in the environment,
	    falling back to "/etc/X11/app-defaults/"
Please copy prologue.ps to one of the above directories
or set the environmental variable GNUPLOT_PS_DIR
or set the loadpath appropriately
"/corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.gp", line 36: Plot failed!

WARNING: Unable to run 'gnuplot /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.gp', Inappropriate ioctl for device
ERROR: PNG file not created.
ERROR: Failed to produce output file(s).
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper/0.0.7, exit_code: 1, stderr: # reading input file "/corral4/main/objects/e/c/5/dataset_ec5ecef7-71ad-4071-b401-017f2ee5e2f8.dat" of length 10734
# construct suffix tree for sequence of length 10734
# (maximum reference length is 2305843009213693948)
# (maximum query length is 18446744073709551615)
# CONSTRUCTIONTIME mummer /corral4/main/objects/e/c/5/dataset_ec5ecef7-71ad-4071-b401-017f2ee5e2f8.dat 0.00
# reading input file "/corral4/main/objects/3/9/c/dataset_39c49fdf-3801-4bd7-989b-efccf3a2760f.dat" of length 10301
# matching query-file "/corral4/main/objects/3/9/c/dataset_39c49fdf-3801-4bd7-989b-efccf3a2760f.dat"
# against subject-file "/corral4/main/objects/e/c/5/dataset_ec5ecef7-71ad-4071-b401-017f2ee5e2f8.dat"
# COMPLETETIME mummer /corral4/main/objects/e/c/5/dataset_ec5ecef7-71ad-4071-b401-017f2ee5e2f8.dat 0.00
# SPACE mummer /corral4/main/objects/e/c/5/dataset_ec5ecef7-71ad-4071-b401-017f2ee5e2f8.dat 0.02
Reading mummer file /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.mums (use mummer -c)
Writing plot files /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.fplot, /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.gp
Rendering plot /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.png

set terminal png tiny size 1400,1400
             ^
"/corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.gp", line 1: unknown or ambiguous terminal type; type just 'set terminal' for a list

WARNING: Unable to run 'gnuplot /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.gp', Inappropriate ioctl for device
Reading mummer file /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.mums (use mummer -c)
Writing plot files /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.fplot, /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.gp
Rendering plot /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.ps
Can't find PostScript prologue file prologue.ps
	loadpath is empty
	gnuplotrc is read from /anaconda/envs/_build/share/gnuplot/4.6
	no XAPPLRESDIR found in the environment,
	    falling back to "/etc/X11/app-defaults/"
Please copy prologue.ps to one of the above directories
or set the environmental variable GNUPLOT_PS_DIR
or set the loadpath appropriately
"/corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.gp", line 36: Plot failed!

WARNING: Unable to run 'gnuplot /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.gp', Inappropriate ioctl for device
ERROR: PNG file not created.
ERROR: Failed to produce output file(s).
.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      1
      

      • 

    

    Standard Error:
    

      

    • 

      # reading input file "/corral4/main/objects/e/c/5/dataset_ec5ecef7-71ad-4071-b401-017f2ee5e2f8.dat" of length 10734
# construct suffix tree for sequence of length 10734
# (maximum reference length is 2305843009213693948)
# (maximum query length is 18446744073709551615)
# CONSTRUCTIONTIME mummer /corral4/main/objects/e/c/5/dataset_ec5ecef7-71ad-4071-b401-017f2ee5e2f8.dat 0.00
# reading input file "/corral4/main/objects/3/9/c/dataset_39c49fdf-3801-4bd7-989b-efccf3a2760f.dat" of length 10301
# matching query-file "/corral4/main/objects/3/9/c/dataset_39c49fdf-3801-4bd7-989b-efccf3a2760f.dat"
# against subject-file "/corral4/main/objects/e/c/5/dataset_ec5ecef7-71ad-4071-b401-017f2ee5e2f8.dat"
# COMPLETETIME mummer /corral4/main/objects/e/c/5/dataset_ec5ecef7-71ad-4071-b401-017f2ee5e2f8.dat 0.00
# SPACE mummer /corral4/main/objects/e/c/5/dataset_ec5ecef7-71ad-4071-b401-017f2ee5e2f8.dat 0.02
Reading mummer file /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.mums (use mummer -c)
Writing plot files /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.fplot, /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.gp
Rendering plot /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.png

set terminal png tiny size 1400,1400
             ^
"/corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.gp", line 1: unknown or ambiguous terminal type; type just 'set terminal' for a list

WARNING: Unable to run 'gnuplot /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.gp', Inappropriate ioctl for device
Reading mummer file /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.mums (use mummer -c)
Writing plot files /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.fplot, /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.gp
Rendering plot /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.ps
Can't find PostScript prologue file prologue.ps
	loadpath is empty
	gnuplotrc is read from /anaconda/envs/_build/share/gnuplot/4.6
	no XAPPLRESDIR found in the environment,
	    falling back to "/etc/X11/app-defaults/"
Please copy prologue.ps to one of the above directories
or set the environmental variable GNUPLOT_PS_DIR
or set the loadpath appropriately
"/corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.gp", line 36: Plot failed!

WARNING: Unable to run 'gnuplot /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.gp', Inappropriate ioctl for device
ERROR: PNG file not created.
ERROR: Failed to produce output file(s).

      

      • 

    

    Standard Output:
    

      

    • 

      gnuplot 4.6 patchlevel 0
gnuplot 4.6 patchlevel 0
mummer -mum -b -c "/corral4/main/objects/e/c/5/dataset_ec5ecef7-71ad-4071-b401-017f2ee5e2f8.dat" "/corral4/main/objects/3/9/c/dataset_39c49fdf-3801-4bd7-989b-efccf3a2760f.dat" > /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.mums
mummerplot -R "/corral4/main/objects/e/c/5/dataset_ec5ecef7-71ad-4071-b401-017f2ee5e2f8.dat" -Q "/corral4/main/objects/3/9/c/dataset_39c49fdf-3801-4bd7-989b-efccf3a2760f.dat" --png --large --prefix=/corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.mums
mummerplot -R "/corral4/main/objects/e/c/5/dataset_ec5ecef7-71ad-4071-b401-017f2ee5e2f8.dat" -Q "/corral4/main/objects/3/9/c/dataset_39c49fdf-3801-4bd7-989b-efccf3a2760f.dat" --postscript --small --prefix=/corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry /corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.mums
ps2pdf -dEPSCrop "/corral4/main/jobs/051/056/51056427/_job_tmp/tmpyrszm0zj/ref_qry.ps" "/corral4/main/objects/6/6/6/dataset_66653fcf-b7a9-4f56-bf29-0bd40dcd7279.dat"

      

      • 

    

    Traceback:
    

      

    • 

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
algorithm
"mummer"

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"fasta"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper (Test test against test.galaxyproject.org #2)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper/0.0.7, exit_code: 1, stderr: 1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "out.ntref" of length 10735
# construct suffix tree for sequence of length 10735
# (maximum reference length is 2305843009213693948)
# (maximum query length is 18446744073709551615)
# CONSTRUCTIONTIME /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.00
# reading input file "/corral4/main/objects/3/9/c/dataset_39c49fdf-3801-4bd7-989b-efccf3a2760f.dat" of length 10301
# matching query-file "/corral4/main/objects/3/9/c/dataset_39c49fdf-3801-4bd7-989b-efccf3a2760f.dat"
# against subject-file "out.ntref"
# COMPLETETIME /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.00
# SPACE /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.02
4: FINISHING DATA
Reading delta file out.delta
Writing plot files /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.fplot, /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.gp
Rendering plot /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.png

set terminal png tiny size 1400,1400
             ^
"/corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.gp", line 1: unknown or ambiguous terminal type; type just 'set terminal' for a list

WARNING: Unable to run 'gnuplot /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.gp', Inappropriate ioctl for device
Reading delta file out.delta
Writing plot files /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.fplot, /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.gp
Rendering plot /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.ps
Can't find PostScript prologue file prologue.ps
	loadpath is empty
	gnuplotrc is read from /anaconda/envs/_build/share/gnuplot/4.6
	no XAPPLRESDIR found in the environment,
	    falling back to "/etc/X11/app-defaults/"
Please copy prologue.ps to one of the above directories
or set the environmental variable GNUPLOT_PS_DIR
or set the loadpath appropriately
"/corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.gp", line 36: Plot failed!

WARNING: Unable to run 'gnuplot /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.gp', Inappropriate ioctl for device
ERROR: PNG file not created.
ERROR: Failed to produce output file(s).
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper/0.0.7, exit_code: 1, stderr: 1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "out.ntref" of length 10735
# construct suffix tree for sequence of length 10735
# (maximum reference length is 2305843009213693948)
# (maximum query length is 18446744073709551615)
# CONSTRUCTIONTIME /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.00
# reading input file "/corral4/main/objects/3/9/c/dataset_39c49fdf-3801-4bd7-989b-efccf3a2760f.dat" of length 10301
# matching query-file "/corral4/main/objects/3/9/c/dataset_39c49fdf-3801-4bd7-989b-efccf3a2760f.dat"
# against subject-file "out.ntref"
# COMPLETETIME /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.00
# SPACE /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.02
4: FINISHING DATA
Reading delta file out.delta
Writing plot files /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.fplot, /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.gp
Rendering plot /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.png

set terminal png tiny size 1400,1400
             ^
"/corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.gp", line 1: unknown or ambiguous terminal type; type just 'set terminal' for a list

WARNING: Unable to run 'gnuplot /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.gp', Inappropriate ioctl for device
Reading delta file out.delta
Writing plot files /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.fplot, /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.gp
Rendering plot /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.ps
Can't find PostScript prologue file prologue.ps
	loadpath is empty
	gnuplotrc is read from /anaconda/envs/_build/share/gnuplot/4.6
	no XAPPLRESDIR found in the environment,
	    falling back to "/etc/X11/app-defaults/"
Please copy prologue.ps to one of the above directories
or set the environmental variable GNUPLOT_PS_DIR
or set the loadpath appropriately
"/corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.gp", line 36: Plot failed!

WARNING: Unable to run 'gnuplot /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.gp', Inappropriate ioctl for device
ERROR: PNG file not created.
ERROR: Failed to produce output file(s).
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper/0.0.7, exit_code: 1, stderr: 1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "out.ntref" of length 10735
# construct suffix tree for sequence of length 10735
# (maximum reference length is 2305843009213693948)
# (maximum query length is 18446744073709551615)
# CONSTRUCTIONTIME /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.00
# reading input file "/corral4/main/objects/3/9/c/dataset_39c49fdf-3801-4bd7-989b-efccf3a2760f.dat" of length 10301
# matching query-file "/corral4/main/objects/3/9/c/dataset_39c49fdf-3801-4bd7-989b-efccf3a2760f.dat"
# against subject-file "out.ntref"
# COMPLETETIME /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.00
# SPACE /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.02
4: FINISHING DATA
Reading delta file out.delta
Writing plot files /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.fplot, /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.gp
Rendering plot /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.png

set terminal png tiny size 1400,1400
             ^
"/corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.gp", line 1: unknown or ambiguous terminal type; type just 'set terminal' for a list

WARNING: Unable to run 'gnuplot /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.gp', Inappropriate ioctl for device
Reading delta file out.delta
Writing plot files /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.fplot, /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.gp
Rendering plot /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.ps
Can't find PostScript prologue file prologue.ps
	loadpath is empty
	gnuplotrc is read from /anaconda/envs/_build/share/gnuplot/4.6
	no XAPPLRESDIR found in the environment,
	    falling back to "/etc/X11/app-defaults/"
Please copy prologue.ps to one of the above directories
or set the environmental variable GNUPLOT_PS_DIR
or set the loadpath appropriately
"/corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.gp", line 36: Plot failed!

WARNING: Unable to run 'gnuplot /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.gp', Inappropriate ioctl for device
ERROR: PNG file not created.
ERROR: Failed to produce output file(s).
.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      1
      

      • 

    

    Standard Error:
    

      

    • 

      1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "out.ntref" of length 10735
# construct suffix tree for sequence of length 10735
# (maximum reference length is 2305843009213693948)
# (maximum query length is 18446744073709551615)
# CONSTRUCTIONTIME /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.00
# reading input file "/corral4/main/objects/3/9/c/dataset_39c49fdf-3801-4bd7-989b-efccf3a2760f.dat" of length 10301
# matching query-file "/corral4/main/objects/3/9/c/dataset_39c49fdf-3801-4bd7-989b-efccf3a2760f.dat"
# against subject-file "out.ntref"
# COMPLETETIME /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.00
# SPACE /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a/opt/mummer-3.23/mummer out.ntref 0.02
4: FINISHING DATA
Reading delta file out.delta
Writing plot files /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.fplot, /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.gp
Rendering plot /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.png

set terminal png tiny size 1400,1400
             ^
"/corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.gp", line 1: unknown or ambiguous terminal type; type just 'set terminal' for a list

WARNING: Unable to run 'gnuplot /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.gp', Inappropriate ioctl for device
Reading delta file out.delta
Writing plot files /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.fplot, /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.rplot
Writing gnuplot script /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.gp
Rendering plot /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.ps
Can't find PostScript prologue file prologue.ps
	loadpath is empty
	gnuplotrc is read from /anaconda/envs/_build/share/gnuplot/4.6
	no XAPPLRESDIR found in the environment,
	    falling back to "/etc/X11/app-defaults/"
Please copy prologue.ps to one of the above directories
or set the environmental variable GNUPLOT_PS_DIR
or set the loadpath appropriately
"/corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.gp", line 36: Plot failed!

WARNING: Unable to run 'gnuplot /corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.gp', Inappropriate ioctl for device
ERROR: PNG file not created.
ERROR: Failed to produce output file(s).

      

      • 

    

    Standard Output:
    

      

    • 

      gnuplot 4.6 patchlevel 0
gnuplot 4.6 patchlevel 0
nucmer "/corral4/main/objects/e/c/5/dataset_ec5ecef7-71ad-4071-b401-017f2ee5e2f8.dat" "/corral4/main/objects/3/9/c/dataset_39c49fdf-3801-4bd7-989b-efccf3a2760f.dat"
mummerplot -R "/corral4/main/objects/e/c/5/dataset_ec5ecef7-71ad-4071-b401-017f2ee5e2f8.dat" -Q "/corral4/main/objects/3/9/c/dataset_39c49fdf-3801-4bd7-989b-efccf3a2760f.dat" --png --large --prefix=/corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry out.delta
mummerplot -R "/corral4/main/objects/e/c/5/dataset_ec5ecef7-71ad-4071-b401-017f2ee5e2f8.dat" -Q "/corral4/main/objects/3/9/c/dataset_39c49fdf-3801-4bd7-989b-efccf3a2760f.dat" --postscript --small --prefix=/corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry out.delta
ps2pdf -dEPSCrop "/corral4/main/jobs/051/056/51056422/_job_tmp/tmpkfnx11qn/ref_qry.ps" "/corral4/main/objects/c/4/a/dataset_c4a9a813-f61a-42b2-8ffc-abb92136d0f0.dat"

      

      • 

    

    Traceback:
    

      

    • 

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
algorithm
"nucmer"

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"fasta"

      
      

      

      • 

    

    

    • 




      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    
















  
  

    

      

  





  




  
  

              

  
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          @mvdbeek 
        
          @jennaj