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test velveth/1.2.10.2 #89

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jennaj opened this issue Mar 22, 2023 · 2 comments
Closed

test velveth/1.2.10.2 #89

jennaj opened this issue Mar 22, 2023 · 2 comments

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@jennaj
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jennaj commented Mar 22, 2023

toolshed.g2.bx.psu.edu/repos/devteam/velvet/velveth/1.2.10.2
@jennaj
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jennaj commented Mar 22, 2023

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/devteam/velvet/velveth/1.2.10.2

@mvdbeek
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mvdbeek commented Mar 23, 2023

Results (powered by Planemo)

Summary

State Count
Total 3
Passed 0
Error 0
Failure 3
Skipped 0
Failed s
  • ❌ toolshed.g2.bx.psu.edu/repos/devteam/velvet/velveth (Test tool test #1)

    Problems:

    • Output outfile: Composite file (Roadmaps) of History item f9cad7b01a472135e5e98369f87f7eb1 different than expected, difference:
History item f9cad7b01a472135e5e98369f87f7eb1 different than expected, difference (using diff):
( /tmp/tmppmcdbnd5Roadmaps v. /tmp/tmprhh8wcfoRoadmaps )
--- local_file
+++ history_data
@@ -1,4 +1,208 @@
 2496	0	21	1
+ROADMAP 833
+ROADMAP 834
+833	0	0	130
+ROADMAP 835
+ROADMAP 836
+835	0	0	130
+ROADMAP 837
+ROADMAP 838
+837	0	0	130
+ROADMAP 839
+ROADMAP 840
+839	0	0	130
+ROADMAP 841
+ROADMAP 842
+841	0	0	130
+ROADMAP 843
+ROADMAP 844
+843	0	0	130
+ROADMAP 845
+ROADMAP 846
+845	0	0	130
********
*SNIP *
********
+135	0	27	38
+827	0	21	42
+135	0	59	99
+827	0	42	57
+-283	0	129	111
+ROADMAP 829
+-2401	0	30	20
+-1745	0	129	97
+1493	0	0	21
+-1745	0	76	53
+ROADMAP 830
+-2401	0	30	20
+-1745	0	129	97
+1493	0	0	21
+-1745	0	76	53
+829	0	0	44
+ROADMAP 831
+-907	0	58	-1
+681	0	0	23
+681	21	44	71
+ROADMAP 832
+-907	0	58	-1
+681	0	0	23
+831	0	0	21
+681	0	44	71

    Command Line:

    • 

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      [0.000000] Reading FastQ file /corral4/main/objects/e/d/2/dataset_ed2eaf5e-f55c-4ee5-ad26-903933225df6.dat;
[0.000251] Reading FastQ file /corral4/main/objects/e/d/2/dataset_ed2eaf5e-f55c-4ee5-ad26-903933225df6.dat;
[0.009949] 2496 sequences found in total in the paired sequence files
[0.009951] Done
[0.022129] Reading read set file /corral4/main/jobs/049/101/49101663/working/dataset_07fe1ff2-3dab-4926-9559-501831a633ff_files/Sequences;
[0.022921] 2496 sequences found
[0.026232] Done
[0.026235] 2496 sequences in total.
[0.028488] Writing into roadmap file /corral4/main/jobs/049/101/49101663/working/dataset_07fe1ff2-3dab-4926-9559-501831a633ff_files/Roadmaps...
[0.032811] Inputting sequences...
[0.033211] Inputting sequence 0 / 2496
[0.103074]  === Sequences loaded in 0.070272 s
[0.103715] Done inputting sequences
[0.103717] Destroying splay table
[0.118057] Splay table destroyed

      

      • 

    

    Traceback:
    

      

    • 

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
hash_length
"21"

      

      
strand_specific
false

      

      
inputs
[{"__index__": 0, "input_type": {"__current_case__": 1, "input": {"values": [{"id": 109691879, "src": "hda"}]}, "input2": {"values": [{"id": 109691879, "src": "hda"}]}, "input_type_selector": "paireds", "read_type": "-shortPaired"}}]

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

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

      

      
dbkey
"?"

      

      
__input_ext
"fastq"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/devteam/velvet/velveth (Test test against test.galaxyproject.org #2)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/devteam/velvet/velveth/1.2.10.2, exit_code: None, stderr: .

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/devteam/velvet/velveth/1.2.10.2, exit_code: None, stderr: .

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Traceback:
    

      

    • 

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
__input_ext
"fastq"

      

      
inputs
[{"__index__": 0, "input_type": {"__current_case__": 0, "input": {"values": [{"id": 109691876, "src": "hda"}]}, "input_type_selector": "single", "read_type": "-short"}}]

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
hash_length
"21"

      

      
strand_specific
false

      

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

      

      
dbkey
"?"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/devteam/velvet/velveth (Test Test Prokka 1.14.6+galaxy1 #3)
    

    Problems:
    

      

    • 

      Output outfile: Composite file (Roadmaps) of History item f9cad7b01a4721353538d8f2e96048ae different than expected, difference:
History item f9cad7b01a4721353538d8f2e96048ae different than expected, difference (using diff):
( /tmp/tmpn1554ubrRoadmaps v. /tmp/tmpif5vj5r_Roadmaps )
--- local_file
+++ history_data
@@ -1,4 +1,44 @@
 2496	0	21	1
+ROADMAP 1249
+ROADMAP 1250
+ROADMAP 1251
+ROADMAP 1252
+ROADMAP 1253
+ROADMAP 1254
+ROADMAP 1255
+ROADMAP 1256
+ROADMAP 1257
+ROADMAP 1258
+ROADMAP 1259
+ROADMAP 1260
+ROADMAP 1261
+ROADMAP 1262
+ROADMAP 1263
+ROADMAP 1264
+-834	0	41	25
+-834	21	4	-1
+ROADMAP 1265
+850	57	0	52
+ROADMAP 1266
********
*SNIP *
********
 -1010	21	14	-1
 ROADMAP 2493
 -126	0	84	-1
--2260	0	95	50
+-2260	0	115	70
 ROADMAP 2494
 1103	0	42	69
-1103	21	90	130
-2150	21	0	32
+2150	21	1	73
 ROADMAP 2495
 51	20	65	67
-674	20	23	44
+-1386	20	13	-1
+674	20	0	7
 51	20	88	130
--1922	61	21	17
+-1922	61	128	124
 ROADMAP 2496
 -2196	0	10	-1
 1399	30	0	53
--1656	30	20	-1
+-2001	30	44	41
+-1656	30	17	-1
 1399	30	74	89


      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      [0.000000] Reading FastQ file /corral4/main/objects/e/d/1/dataset_ed1b33f1-aa0d-46e2-997b-5b893e2df62c.dat;
[0.005038] 1248 sequences found
[0.005040] Done
[0.037425] Reading FastQ file /corral4/main/objects/e/d/2/dataset_ed2eaf5e-f55c-4ee5-ad26-903933225df6.dat;
[0.043651] 1248 sequences found
[0.043653] Done
[0.055993] Reading read set file /corral4/main/jobs/049/101/49101664/working/dataset_920b2bea-7d32-4ee8-8a21-ba1e3c3cb0b8_files/Sequences;
[0.056767] 2496 sequences found
[0.060041] Done
[0.060045] 2496 sequences in total.
[0.065534] Writing into roadmap file /corral4/main/jobs/049/101/49101664/working/dataset_920b2bea-7d32-4ee8-8a21-ba1e3c3cb0b8_files/Roadmaps...
[0.070116] Inputting sequences...
[0.070484] Inputting sequence 0 / 2496
[0.145201]  === Sequences loaded in 0.075095 s
[0.145985] Done inputting sequences
[0.145987] Destroying splay table
[0.161288] Splay table destroyed

      

      • 

    

    Traceback:
    

      

    • 

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
hash_length
"21"

      

      
strand_specific
false

      

      
inputs
[{"__index__": 0, "input_type": {"__current_case__": 0, "input": {"values": [{"id": 109691876, "src": "hda"}]}, "input_type_selector": "single", "read_type": "-short"}}, {"__index__": 1, "input_type": {"__current_case__": 0, "input": {"values": [{"id": 109691879, "src": "hda"}]}, "input_type_selector": "single", "read_type": "-short2"}}]

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

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

      

      
dbkey
"?"

      

      
__input_ext
"fastq"

      
      

      

      • 

    

    

    • 




      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
            

    

      
    

    


      

          @jennaj
jennaj




            closed this as completed


      Mar 30, 2023

    

  


    











  
  

    

      

  





  




  
  

              

  
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      2 participants
    

    

        
          @mvdbeek 
        
          @jennaj