Test mafft 7.221.3 #12

jennaj · 2022-02-07T21:15:21Z

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.221.3

mvdbeek · 2022-02-07T21:16:22Z

You'll have add these as a comment

mvdbeek · 2022-02-07T21:16:28Z

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.221.3

mvdbeek · 2022-02-07T21:18:00Z

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/rnateam/mafft/rbc_mafft (Test tool test #1)

Problems:

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.221.3, exit_code: None, stderr: .

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.221.3, exit_code: None, stderr: .

Command Line:

Job Parameters:

Job parameter	Parameter value
datatype	`""`
cond_flavour	`{"__current_case__": 0, "flavourType": "mafft-fftns"}`
ep	`"0.123"`
op	`"1.53"`
adjustdirection	`" "`
matrix_condition	`{"__current_case__": 0, "matrix": ""}`
reorder	`"false"`
getTree	`"false"`
outputFormat	`""`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"fasta"`

❌ toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft (Test test against test.galaxyproject.org #2)

Problems:

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.221.3, exit_code: None, stderr: .

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.221.3, exit_code: None, stderr: .

Command Line:

Job Parameters:

Job parameter	Parameter value
datatype	`""`
cond_flavour	`{"__current_case__": 3, "flavourType": "mafft-nwns"}`
ep	`"0.123"`
op	`"1.53"`
adjustdirection	`" "`
matrix_condition	`{"__current_case__": 0, "matrix": ""}`
reorder	`"false"`
getTree	`"false"`
outputFormat	`"--clustalout"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"fasta"`

jennaj · 2022-02-08T03:26:30Z

Ticket to install latest version galaxyproject/usegalaxy-playbook#351

jennaj · 2022-02-08T19:35:33Z

PR galaxyproject/usegalaxy-tools#467

jennaj · 2022-02-09T01:39:59Z

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.489+galaxy0

mvdbeek · 2022-02-09T01:41:22Z

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/rnateam/mafft/rbc_mafft (Test tool test #1)

Problems:

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.221.3, exit_code: None, stderr: .

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.221.3, exit_code: None, stderr: .

Command Line:

Job Parameters:

Job parameter	Parameter value
datatype	`""`
cond_flavour	`{"__current_case__": 0, "flavourType": "mafft-fftns"}`
ep	`"0.123"`
op	`"1.53"`
adjustdirection	`" "`
matrix_condition	`{"__current_case__": 0, "matrix": ""}`
reorder	`"false"`
getTree	`"false"`
outputFormat	`""`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"fasta"`

❌ toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft (Test test against test.galaxyproject.org #2)

Problems:

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.221.3, exit_code: None, stderr: .

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.221.3, exit_code: None, stderr: .

Command Line:

Job Parameters:

Job parameter	Parameter value
datatype	`""`
cond_flavour	`{"__current_case__": 3, "flavourType": "mafft-nwns"}`
ep	`"0.123"`
op	`"1.53"`
adjustdirection	`" "`
matrix_condition	`{"__current_case__": 0, "matrix": ""}`
reorder	`"false"`
getTree	`"false"`
outputFormat	`"--clustalout"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"fasta"`

jennaj · 2022-02-14T19:01:20Z

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.489+galaxy0

mvdbeek · 2022-02-14T19:03:34Z

Results (powered by Planemo)

Summary

State	Count
Total	3
Passed	2
Error	0
Failure	1
Skipped	0

Failed s

❌ toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft (Test Test Prokka 1.14.6+galaxy1 #3)

Problems:

Output outputAlignment:  different than expected, difference (using diff):
( /tmp/tmpv_co1rjbmafft_custom_result.aln v. /tmp/tmpaz9bjftjmafft_custom_result.aln )
--- local_file
+++ history_data
@@ -1,233 +1,233 @@
-CLUSTAL format alignment by MAFFT F-INS-i (v7.455)
-
-
-1==             MN------------------------GTE--GDNFYVPFS--------NKTGL-ARSPYE
-2==             MN------------------------GTE--GPNFYVPFS--------NITGV-VRSPFE
-3==             MN------------------------GTE--GINFYVPMS--------NKTGV-VRSPFE
-4=p             MN------------------------GTE--GKNFYVPMS--------NRTGL-VRSPFE
-5=p             MN------------------------GTE--GNNFYVPLS--------NRTGL-VRSPFE
-6==             MK------------------------QVPEFHEDFYIPIP-------LDINNLSAYSPFL
-7==             MR------------------------KMS--EEEFYL------------FKNISSVGPWD
-8=opsin,        ------------------------------------------------------------
-9==             MAQQWSLQ-RLAGRHPQDS----YEDSTQ--SSIFTYTNS--------NS----TRGPFE
-10==            MAQQWSLQ-RLAGRHPQDS----YEDSTQ--SSIFTYTNS--------NS----TRGPFE
-11==            MTEAWNVAVFAARRSRDD------DDTTR--GSVFTYTNT--------NN----TRGPFE
-12==            MA-AWEAA-FAARRRHEE------EDTTR--DSVFTYTNS--------NN----TRGPFE
-13==            MS----------------------SNSSQ--------------AP--PNG----TPGPFD
-14==            MESG-NV-----------------------------------------SSSLFGNVSTAL
-15==            MEYH-NV------------------------------------------SSVLGNVSSVL
-16==            MEPLCNA------------------------------------------------SEPPL
-17==            MDALCNA------------------------------------------------SEPPL
-18==            MT-------------------------------------------------------NAT
-19==            MA-------------------------------------------------------NVT
********
*SNIP *
********
+13==            -------------------------------------------KVMP-A-------HPV
+14==            -------------------------------------------QTTA-A----------
+15==            -------------------------------------------QTTA-A----------
+16==            -------------------------------------------QTTA-A----------
+17==            -------------------------------------------QTSA-A----------
+18==            ------------------------------------------------A----------
+19==            ------------------------------------------------S----------
+20==            ---------------------------------------------SK-A----------
+21==            ---------------------------------------------SK-A----------
+22==            ---------------------------------------------SK-A----------
+23==            ---------------------------------------------SK-A----------
+24==            ---------------------------------------------SK-D----------
+25==            ---------------------------EK----------------SN-A----------
+26==            ---------------------------PK---------------IPE-A----------
+27==            PPPQGYPPQGYPPQGYPPQGYPPQGAPPQVEAPQGAPPQGVDNQAYQ-A----------
+28==            PP-QGYPPQGYPPQGYPP---PPQGAPPQ-GAPPAAPPQGVDNQAYQ-A----------
+29==            ---------------------------PE--------------FVLQNADYCRKKGHDS
+30==            ---------------------------SE--------------FVLQNSDHCGKKGHDT
+31=p            ---------------------------SE--------------FVLQNSDHCGKKGHDT
+32==            -----------------------------------------------------------
+33=p            -----------------------------------------------------------
+34==            -----------------------------------------------------------
+35=p            -----------------------------------------------------------
+36==            ------------------------------------------------APQ--------
+

Command Line:

Exit Code:

```
0
```

Standard Error:

rescale = 1
query :    1 /    36
query :    2 /    36
query :    3 /    36
query :    4 /    36
query :    5 /    36
query :    6 /    36
query :    7 /    36
query :    8 /    36
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query :   19 /    36
query :   20 /    36
query :   21 /    36
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query :   23 /    36
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query :   27 /    36
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query :   29 /    36
query :   30 /    36
query :   31 /    36
query :   32 /    36
query :   33 /    36
query :   34 /    36
query :   35 /    36
query :   36 /    36
##### writing hat3
dndfast7 (aa) Version 7.489
alg=, model=BLOSUM62, -0.00, -0.00, -0.00, noshift, amax=0.0
1 thread(s)

treein = 0
compacttree = 0
stacksize: -1 kb
Loading 'hat3' ... 
done.
rescale = 1
Gap Penalty = -1.53, +0.00, +0.00
tbutree = 1, compacttree = 0
Loading 'hat2' ... done.
Constructing a UPGMA tree ... 

    0 / 36
   10 / 36
   20 / 36
   30 / 36
done.

Progressive alignment ... 

STEP     1 /35 (thread    2) 
STEP     2 /35 (thread    1) 
STEP     3 /35 (thread    0) 
STEP     5 /35 (thread    3) 
STEP     7 /35 (thread    0) 
STEP     4 /35 (thread    4) 
STEP     8 /35 (thread    3) 
STEP     9 /35 (thread    0) 
STEP    10 /35 (thread    1) 
STEP     6 /35 (thread    5) 
STEP    12 /35 (thread    0) 
STEP    14 /35 (thread    0) 
STEP    15 /35 (thread    0) 
STEP    11 /35 (thread    3) 
STEP    17 /35 (thread    2) 
STEP    18 /35 (thread    0) 
STEP    16 /35 (thread    4) 
STEP    19 /35 (thread    5) 
STEP    20 /35 (thread    3) 
STEP    21 /35 (thread    2) 
STEP    13 /35 (thread    1) 
STEP    23 /35 (thread    5) 
STEP    22 /35 (thread    4) 
STEP    26 /35 (thread    0) 
STEP    24 /35 (thread    3) 
STEP    25 /35 (thread    2) 
STEP    31 /35 (thread    3) 
STEP    27 /35 (thread    1) 
STEP    28 /35 (thread    5) 
STEP    32 /35 (thread    2) 
STEP    29 /35 (thread    0) 
STEP    30 /35 (thread    4) 
STEP    34 /35 (thread    3) 
STEP    33 /35 (thread    1) 
Reallocating (by thread 5) ..done. *alloclen = 2122

STEP    35 /35 (thread    5) 
done.
tbfast (aa) Version 7.489
alg=A, model=BLOSUM62, 1.53, -0.00, -0.00, noshift, amax=0.0
6 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 6
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 16
sueff_global = 0.100000
nadd = 16
Loading 'hat3' ... done.
rescale = 1


    0 / 36
   10 / 36
   20 / 36
   30 / 36
Segment   1/  1    1- 714
001-0000-1 (thread    6) identical     

001-0001-0 (thread    3) identical     

001-0002-1 (thread    1) identical     

001-0003-1 (thread    5) identical     

001-0004-0 (thread    2) identical     

001-0005-1 (thread    3) identical     

001-0005-0 (thread    6) identical     

001-0007-0 (thread    1) identical     

001-0008-0 (thread    4) identical     

001-0009-1 (thread    5) identical     

001-0010-1 (thread    3) identical     

001-0011-0 (thread    6) identical     

001-0012-1 (thread    1) identical     

001-0013-0 (thread    3) identical     

001-0014-0 (thread    2) identical     
001-0014-0 (thread    2) better     

001-0015-1 (thread    3) identical     
001-0015-1 (thread    3) worse      

001-0016-1 (thread    6) identical     

001-0017-1 (thread    5) identical     
001-0017-0 (thread    1) identical     

001-0018-1 (thread    5) worse      

001-0019-1 (thread    3) identical     

001-0020-0 (thread    6) identical     

001-0021-0 (thread    4) identical     

001-0022-1 (thread    3) identical     

001-0023-0 (thread    2) identical     

001-0024-1 (thread    1) identical     

001-0025-0 (thread    5) identical     

001-0026-0 (thread    3) identical     

001-0027-0 (thread    6) identical     

001-0028-0 (thread    1) identical     

001-0029-0 (thread    3) identical     

001-0030-1 (thread    4) identical     

001-0031-1 (thread    2) identical     

001-0031-1 (thread    5) identical     

001-0033-1 (thread    6) identical     

001-0034-1 (thread    3) identical     
001-0034-1 (thread    3) worse      

001-0035-0 (thread    1) identical     

001-0036-0 (thread    5) identical     

001-0037-1 (thread    6) identical     
001-0037-1 (thread    6) worse      

001-0038-0 (thread    3) identical     
001-0038-0 (thread    3) worse      

001-0039-1 (thread    1) identical     
001-0039-1 (thread    1) worse      

001-0040-1 (thread    2) identical     
001-0040-1 (thread    2) worse      

001-0041-0 (thread    5) identical     

001-0042-1 (thread    6) identical     
001-0042-1 (thread    6) worse      

001-0043-0 (thread    4) identical     
001-0043-0 (thread    4) worse      

001-0044-0 (thread    3) identical     
001-0044-0 (thread    3) better     

001-0045-0 (thread    6) identical     

001-0046-1 (thread    1) identical     
001-0046-1 (thread    1) worse      

001-0047-1 (thread    5) identical     
001-0047-1 (thread    5) worse      

001-0048-1 (thread    4) identical     

001-0049-0 (thread    3) identical     

001-0050-1 (thread    6) identical     

001-0051-0 (thread    1) identical     
001-0051-1 (thread    5) identical     
001-0051-0 (thread    1) worse      

001-0052-0 (thread    2) identical     

001-0052-1 (thread    5) worse      

001-0054-1 (thread    3) identical     

001-0055-0 (thread    4) identical     
001-0055-0 (thread    4) worse      

001-0056-0 (thread    6) identical     
001-0056-0 (thread    6) worse      

001-0057-1 (thread    1) identical     
001-0057-1 (thread    1) worse      

001-0058-0 (thread    3) identical     
001-0058-0 (thread    3) worse      

001-0059-1 (thread    5) identical     
001-0059-1 (thread    5) worse      

001-0060-0 (thread    2) identical     
001-0060-0 (thread    2) worse      

001-0061-0 (thread    3) identical     
001-0061-0 (thread    3) worse      

001-0062-0 (thread    6) identical     
001-0062-0 (thread    6) worse      

001-0063-1 (thread    1) identical     
001-0063-1 (thread    1) better     

001-0064-1 (thread    3) identical     
001-0064-1 (thread    3) worse      

001-0065-1 (thread    5) identical     
001-0065-1 (thread    5) better     

001-0066-1 (thread    6) identical     
001-0066-1 (thread    6) worse      

001-0067-0 (thread    2) identical     
001-0067-0 (thread    2) better     

001-0068-1 (thread    4) identical     
001-0068-1 (thread    4) better     

002-0000-0 (thread    6) identical     

002-0001-0 (thread    3) identical     

002-0002-1 (thread    4) identical     

002-0003-1 (thread    2) identical     

002-0004-0 (thread    5) identical     

002-0005-0 (thread    6) identical     

002-0006-0 (thread    4) identical     

002-0007-1 (thread    2) identical     

002-0008-1 (thread    3) identical     

002-0009-1 (thread    1) identical     

002-0010-1 (thread    6) identical     

002-0011-0 (thread    4) identical     

002-0011-1 (thread    2) identical     

002-0013-0 (thread    5) identical     
002-0013-0 (thread    5) better     

002-0014-0 (thread    6) identical     

002-0015-0 (thread    2) identical     

002-0016-1 (thread    4) identical     

002-0017-0 (thread    3) identical     

002-0018-1 (thread    5) identical     
002-0018-1 (thread    5) worse      

002-0019-1 (thread    1) identical     
002-0019-1 (thread    1) worse      

002-0020-0 (thread    6) identical     

002-0021-1 (thread    2) identical     

002-0022-0 (thread    4) identical     

002-0023-1 (thread    3) identical     

002-0024-0 (thread    6) identical     

002-0025-1 (thread    1) identical     

002-0026-1 (thread    2) identical     

002-0027-0 (thread    4) identical     

002-0028-0 (thread    5) identical     

002-0029-1 (thread    3) identical     

002-0030-0 (thread    6) identical     

002-0031-0 (thread    2) identical     

002-0032-1 (thread    4) identical     

002-0033-1 (thread    1) identical     

002-0034-0 (thread    6) identical     
002-0034-0 (thread    6) worse      

002-0035-1 (thread    3) identical     
002-0035-1 (thread    3) worse      

002-0036-0 (thread    5) identical     

002-0037-0 (thread    4) identical     

002-0038-1 (thread    2) identical     
002-0038-1 (thread    2) worse      

002-0039-0 (thread    6) identical     
002-0039-0 (thread    6) worse      

002-0040-1 (thread    1) identical     
002-0040-1 (thread    1) worse      

002-0041-1 (thread    3) identical     
002-0041-1 (thread    3) worse      

002-0042-1 (thread    4) identical     
002-0042-1 (thread    4) worse      

002-0043-1 (thread    6) identical     
002-0043-1 (thread    6) worse      

002-0044-0 (thread    5) identical     

002-0045-0 (thread    2) identical     

002-0046-0 (thread    4) identical     

002-0047-1 (thread    3) identical     
002-0047-1 (thread    3) worse      

002-0048-1 (thread    6) identical     

002-0049-1 (thread    2) identical     
002-0049-1 (thread    2) worse      

002-0050-0 (thread    1) identical     

002-0051-0 (thread    4) identical     
002-0051-0 (thread    4) worse      

002-0052-0 (thread    5) identical     

002-0053-1 (thread    3) identical     

002-0054-0 (thread    6) identical     
002-0054-0 (thread    6) worse      

002-0055-1 (thread    2) identical     

002-0056-1 (thread    4) identical     
002-0056-1 (thread    4) worse      

002-0057-0 (thread    6) identical     
002-0057-0 (thread    6) better     

002-0058-1 (thread    2) identical     
002-0058-1 (thread    2) better     

002-0059-0 (thread    4) identical     
002-0059-0 (thread    4) better     

002-0060-1 (thread    3) identical     
002-0060-1 (thread    3) worse      

002-0061-0 (thread    2) identical     
002-0061-1 (thread    6) identical     
002-0061-1 (thread    6) better     

002-0062-0 (thread    2) worse      

002-0063-0 (thread    3) identical     
002-0063-0 (thread    3) worse      

002-0064-1 (thread    6) identical     
002-0064-1 (thread    6) better     

002-0065-0 (thread    5) identical     
002-0065-1 (thread    2) identical     

002-0066-0 (thread    5) worse      

002-0067-0 (thread    1) identical     
002-0067-1 (thread    4) identical     
002-0067-0 (thread    1) worse      

002-0068-1 (thread    4) worse      

003-0000-0 (thread    3) identical     

003-0001-0 (thread    4) identical     

003-0002-0 (thread    2) identical     

003-0003-1 (thread    1) identical     

003-0004-1 (thread    5) identical     

003-0004-1 (thread    6) identical     

003-0006-0 (thread    3) identical     

003-0007-1 (thread    4) identical     

003-0008-1 (thread    1) identical     

003-0009-0 (thread    2) identical     

003-0010-1 (thread    6) identical     

003-0011-0 (thread    5) identical     

003-0012-0 (thread    3) identical     

003-0013-1 (thread    4) identical     

003-0014-1 (thread    2) identical     
003-0014-0 (thread    1) identical     

003-0015-1 (thread    2) worse      

003-0016-0 (thread    6) identical     

003-0017-1 (thread    5) identical     

003-0018-0 (thread    3) identical     

003-0019-1 (thread    4) identical     
003-0019-1 (thread    4) worse      

003-0020-1 (thread    2) identical     

003-0021-0 (thread    6) identical     

003-0022-1 (thread    5) identical     

003-0023-0 (thread    1) identical     

003-0024-1 (thread    4) identical     

003-0025-0 (thread    3) identical     

003-0026-0 (thread    2) identical     

003-0027-1 (thread    6) identical     

003-0028-0 (thread    5) identical     

003-0029-1 (thread    1) identical     

003-0030-1 (thread    3) identical     

003-0031-0 (thread    4) identical     

003-0032-0 (thread    2) identical     

003-0033-1 (thread    6) identical     

003-0034-0 (thread    5) identical     
003-0034-0 (thread    5) worse      

003-0035-1 (thread    1) identical     
003-0035-1 (thread    1) worse      

003-0036-0 (thread    3) identical     
003-0036-0 (thread    3) worse      

003-0037-0 (thread    2) identical     

003-0038-1 (thread    6) identical     
003-0038-1 (thread    6) worse      

003-0039-1 (thread    4) identical     
003-0039-1 (thread    4) worse      

003-0040-0 (thread    5) identical     
003-0040-0 (thread    5) worse      

003-0041-1 (thread    1) identical     
003-0041-1 (thread    1) worse      

003-0042-0 (thread    3) identical     

003-0043-1 (thread    4) identical     
003-0043-1 (thread    4) worse      

003-0044-1 (thread    2) identical     
003-0044-1 (thread    2) worse      

003-0045-0 (thread    3) identical     

003-0046-0 (thread    6) identical     

003-0047-1 (thread    1) identical     
003-0047-1 (thread    1) worse      

003-0048-1 (thread    4) identical     

003-0049-0 (thread    5) identical     

003-0050-1 (thread    3) identical     
003-0050-1 (thread    3) worse      

003-0051-0 (thread    2) identical     

003-0052-0 (thread    6) identical     

003-0053-1 (thread    1) identical     

003-0054-0 (thread    4) identical     
003-0054-0 (thread    4) better     

003-0055-0 (thread    3) identical     

003-0056-0 (thread    6) identical     
003-0056-0 (thread    4) identical     
003-0056-0 (thread    4) better     

003-0057-0 (thread    6) worse      

003-0058-1 (thread    3) identical     
003-0058-1 (thread    3) worse      

003-0059-1 (thread    2) identical     
003-0059-1 (thread    2) worse      

003-0060-1 (thread    5) identical     
003-0060-0 (thread    4) identical     
003-0060-1 (thread    5) worse      

003-0061-0 (thread    4) better     

003-0062-1 (thread    4) identical     
003-0062-1 (thread    6) identical     
003-0062-1 (thread    4) worse      

003-0063-1 (thread    6) worse      

003-0064-0 (thread    3) identical     
003-0064-0 (thread    3) worse      

003-0065-1 (thread    1) identical     

003-0066-0 (thread    5) identical     
003-0066-0 (thread    5) worse      

003-0067-1 (thread    2) identical     
003-0067-1 (thread    2) worse      

003-0068-1 (thread    4) identical     
003-0068-1 (thread    4) worse      

004-0000-0 (thread    3) identical     

004-0001-0 (thread    5) identical     

004-0002-1 (thread    4) identical     

004-0003-1 (thread    2) identical     

004-0004-0 (thread    1) identical     

004-0005-1 (thread    6) identical     

004-0006-0 (thread    3) identical     

004-0007-1 (thread    5) identical     

004-0008-0 (thread    4) identical     

004-0009-1 (thread    2) identical     

004-0010-0 (thread    1) identical     
004-0010-0 (thread    1) worse      

004-0011-1 (thread    6) identical     

004-0012-0 (thread    3) identical     

004-0013-1 (thread    5) identical     

004-0014-0 (thread    1) identical     

004-0015-0 (thread    4) identical     

004-0016-1 (thread    2) identical     
004-0016-1 (thread    2) worse      

004-0017-1 (thread    6) identical     

004-0018-0 (thread    3) identical     

004-0019-1 (thread    5) identical     
004-0019-1 (thread    5) worse      

004-0020-1 (thread    4) identical     

004-0021-0 (thread    2) identical     

004-0022-1 (thread    6) identical     

004-0023-0 (thread    1) identical     

004-0024-0 (thread    3) identical     

004-0025-1 (thread    5) identical     

004-0026-0 (thread    4) identical     

004-0027-1 (thread    2) identical     

004-0028-0 (thread    6) identical     

004-0029-1 (thread    1) identical     

004-0030-0 (thread    3) identical     

004-0031-0 (thread    4) identical     

004-0032-1 (thread    5) identical     

004-0033-1 (thread    2) identical     

004-0034-0 (thread    6) identical     
004-0034-0 (thread    6) worse      

004-0035-1 (thread    1) identical     
004-0035-1 (thread    1) worse      

004-0036-0 (thread    3) identical     
004-0036-0 (thread    3) worse      

004-0037-0 (thread    5) identical     

004-0038-1 (thread    2) identical     
004-0038-1 (thread    2) worse      

004-0039-1 (thread    4) identical     
004-0039-1 (thread    4) worse      

004-0040-0 (thread    6) identical     
004-0040-0 (thread    6) worse      

004-0041-1 (thread    1) identical     
004-0041-1 (thread    1) worse      

004-0042-0 (thread    3) identical     

004-0043-1 (thread    5) identical     
004-0043-1 (thread    5) worse      

004-0044-1 (thread    4) identical     
004-0044-1 (thread    4) worse      

004-0045-0 (thread    3) identical     

004-0046-0 (thread    2) identical     

004-0047-1 (thread    1) identical     
004-0047-1 (thread    1) better     

004-0048-1 (thread    3) identical     
004-0048-1 (thread    5) identical     

004-0049-1 (thread    3) worse      

004-0050-0 (thread    6) identical     

004-0051-0 (thread    4) identical     

004-0052-1 (thread    1) identical     

004-0053-0 (thread    2) identical     
004-0053-0 (thread    2) worse      

004-0054-0 (thread    5) identical     

004-0055-1 (thread    3) identical     
004-0055-1 (thread    3) worse      

004-0056-0 (thread    6) identical     

004-0057-0 (thread    1) identical     
004-0057-0 (thread    1) worse      

004-0058-1 (thread    2) identical     

004-0059-0 (thread    5) identical     
004-0059-0 (thread    5) better     

004-0060-1 (thread    3) identical     
004-0060-1 (thread    3) better     

004-0061-0 (thread    3) identical     
004-0061-0 (thread    3) better     

004-0062-1 (thread    3) identical     
004-0062-1 (thread    3) better     

004-0063-1 (thread    3) identical     
004-0063-0 (thread    2) identical     
004-0063-0 (thread    6) identical     
004-0063-1 (thread    3) worse      

004-0064-0 (thread    6) better     

004-0065-0 (thread    2) worse      

004-0066-1 (thread    1) identical     
004-0066-1 (thread    1) better     

004-0067-1 (thread    5) identical     
004-0067-1 (thread    5) worse      

004-0068-1 (thread    4) identical     
004-0068-1 (thread    4) worse      

005-0000-0 (thread    6) identical     

005-0001-1 (thread    3) identical     

005-0001-1 (thread    1) identical     

005-0002-1 (thread    5) identical     

005-0004-0 (thread    2) identical     

005-0005-0 (thread    4) identical     

005-0006-1 (thread    3) identical     

005-0007-1 (thread    5) identical     

005-0008-0 (thread    2) identical     
005-0008-0 (thread    1) identical     

005-0008-0 (thread    2) worse      

005-0010-0 (thread    6) identical     

005-0011-0 (thread    3) identical     

005-0012-1 (thread    5) identical     

005-0013-0 (thread    6) identical     

005-0014-1 (thread    2) identical     
005-0014-1 (thread    2) worse      

005-0015-0 (thread    1) identical     

005-0016-1 (thread    4) identical     

005-0017-1 (thread    3) identical     

005-0018-0 (thread    5) identical     

005-0019-1 (thread    6) identical     
005-0019-1 (thread    6) worse      

005-0020-1 (thread    1) identical     
005-0020-1 (thread    1) better     

005-0021-1 (thread    3) identical     

005-0022-0 (thread    1) identical     

005-0023-1 (thread    6) identical     

005-0024-0 (thread    2) identical     

005-0025-0 (thread    4) identical     

005-0026-0 (thread    5) identical     

005-0027-1 (thread    3) identical     

005-0028-0 (thread    1) identical     

005-0029-1 (thread    6) identical     

005-0030-0 (thread    2) identical     

005-0031-0 (thread    5) identical     

005-0032-1 (thread    3) identical     

005-0033-1 (thread    4) identical     

005-0034-0 (thread    1) identical     
005-0034-0 (thread    1) worse      
005-0034-1 (thread    6) identical     

005-0035-1 (thread    6) worse      

005-0036-0 (thread    3) identical     

005-0037-0 (thread    2) identical     
005-0037-0 (thread    2) worse      

005-0038-1 (thread    5) identical     
005-0038-1 (thread    5) worse      

005-0039-0 (thread    1) identical     
005-0039-0 (thread    1) worse      

005-0040-1 (thread    6) identical     
005-0040-1 (thread    6) worse      

005-0041-1 (thread    4) identical     
005-0041-1 (thread    4) worse      

005-0042-0 (thread    3) identical     

005-0043-1 (thread    2) identical     
005-0043-1 (thread    2) worse      

005-0044-1 (thread    1) identical     
005-0044-1 (thread    1) worse      

005-0045-0 (thread    3) identical     

005-0046-0 (thread    5) identical     

005-0047-1 (thread    4) identical     
005-0047-1 (thread    4) worse      

005-0048-0 (thread    6) identical     

005-0049-1 (thread    2) identical     

005-0050-1 (thread    3) identical     
005-0050-1 (thread    3) worse      

005-0051-0 (thread    1) identical     
005-0051-0 (thread    1) worse      

005-0052-0 (thread    5) identical     
005-0052-0 (thread    5) worse      

005-0053-0 (thread    6) identical     

005-0054-1 (thread    4) identical     

005-0055-1 (thread    2) identical     
005-0055-1 (thread    2) worse      

005-0056-0 (thread    3) identical     

005-0057-1 (thread    1) identical     
005-0057-1 (thread    1) worse      

005-0058-0 (thread    5) identical     
005-0058-0 (thread    5) worse      

005-0059-1 (thread    6) identical     

005-0060-1 (thread    2) identical     
005-0060-1 (thread    2) worse      

005-0061-0 (thread    3) identical     
005-0061-0 (thread    3) better     

005-0062-1 (thread    3) identical     
005-0062-1 (thread    3) worse      

005-0063-0 (thread    5) identical     
005-0063-0 (thread    5) worse      

005-0064-1 (thread    1) identical     
005-0064-1 (thread    1) better     

005-0065-0 (thread    2) identical     
005-0065-0 (thread    2) worse      

005-0066-0 (thread    4) identical     
005-0066-0 (thread    4) worse      

005-0067-1 (thread    3) identical     
005-0067-1 (thread    6) identical     
005-0067-1 (thread    3) worse      

005-0068-1 (thread    6) worse      

006-0000-0 (thread    6) identical     

006-0001-1 (thread    2) identical     

006-0002-1 (thread    3) identical     

006-0003-0 (thread    1) identical     

006-0004-0 (thread    4) identical     

006-0005-1 (thread    5) identical     

006-0006-1 (thread    2) identical     

006-0007-0 (thread    3) identical     

006-0008-1 (thread    1) identical     

006-0009-0 (thread    6) identical     

006-0010-1 (thread    5) identical     

006-0011-0 (thread    4) identical     

006-0012-1 (thread    3) identical     

006-0013-0 (thread    2) identical     

006-0014-0 (thread    5) identical     

006-0015-0 (thread    1) identical     

006-0016-1 (thread    6) identical     
006-0016-1 (thread    6) worse      

006-0017-1 (thread    4) identical     

006-0018-0 (thread    3) identical     

006-0019-1 (thread    2) identical     
006-0019-1 (thread    2) worse      

006-0020-1 (thread    1) identical     

006-0021-0 (thread    6) identical     

006-0022-0 (thread    5) identical     

006-0023-1 (thread    4) identical     

006-0024-1 (thread    2) identical     

006-0025-0 (thread    3) identical     

006-0026-0 (thread    1) identical     

006-0027-1 (thread    6) identical     

006-0028-0 (thread    5) identical     

006-0029-1 (thread    4) identical     

006-0030-0 (thread    2) identical     

006-0031-1 (thread    3) identical     

006-0032-0 (thread    1) identical     

006-0033-1 (thread    6) identical     

006-0034-0 (thread    5) identical     
006-0034-0 (thread    5) worse      

006-0035-0 (thread    1) identical     

006-0036-1 (thread    6) identical     
006-0036-1 (thread    6) worse      

006-0037-0 (thread    2) identical     
006-0037-1 (thread    4) identical     
006-0037-1 (thread    4) worse      

006-0038-0 (thread    2) worse      

006-0039-1 (thread    3) identical     
006-0039-1 (thread    3) worse      

006-0040-0 (thread    5) identical     
006-0040-0 (thread    5) worse      

006-0041-1 (thread    1) identical     
006-0041-1 (thread    1) worse      

006-0042-1 (thread    3) identical     
006-0042-1 (thread    3) worse      

006-0043-0 (thread    6) identical     

006-0044-1 (thread    4) identical     
006-0044-1 (thread    4) worse      

006-0045-0 (thread    2) identical     
006-0045-0 (thread    2) worse      

006-0046-0 (thread    3) identical     

006-0047-1 (thread    1) identical     
006-0047-1 (thread    1) worse      

006-0048-0 (thread    5) identical     
006-0048-0 (thread    5) better     

006-0049-1 (thread    6) identical     

006-0050-1 (thread    2) identical     
006-0050-1 (thread    2) worse      

006-0051-0 (thread    5) identical     

006-0052-0 (thread    3) identical     
006-0052-0 (thread    3) worse      

006-0053-0 (thread    4) identical     
006-0053-1 (thread    1) identical     

006-0053-0 (thread    4) worse      

006-0055-1 (thread    6) identical     
006-0055-1 (thread    5) identical     
006-0055-1 (thread    5) worse      

006-0055-1 (thread    6) worse      

006-0057-0 (thread    3) identical     
006-0057-0 (thread    3) worse      

006-0058-0 (thread    2) identical     

006-0059-0 (thread    4) identical     
006-0059-0 (thread    4) worse      

006-0060-1 (thread    1) identical     

006-0061-1 (thread    5) identical     
006-0061-1 (thread    5) better     

006-0062-1 (thread    3) identical     
006-0062-1 (thread    3) worse      

006-0063-1 (thread    4) identical     
006-0063-0 (thread    2) identical     
006-0063-0 (thread    1) identical     
006-0063-0 (thread    1) worse      

006-0064-0 (thread    6) identical     
006-0064-1 (thread    5) identical     
006-0064-0 (thread    2) worse      

006-0065-1 (thread    4) worse      

006-0066-0 (thread    6) worse      

006-0067-1 (thread    5) worse      

006-0068-1 (thread    3) identical     

007-0000-1 (thread    3) identical     

007-0001-1 (thread    4) identical     

007-0002-0 (thread    5) identical     

007-0003-0 (thread    2) identical     

007-0004-0 (thread    1) identical     

007-0004-1 (thread    6) identical     

007-0006-1 (thread    4) identical     

007-0007-0 (thread    3) identical     

007-0008-0 (thread    5) identical     

007-0009-1 (thread    2) identical     

007-0010-0 (thread    1) identical     
007-0010-0 (thread    1) worse      

007-0011-1 (thread    6) identical     

007-0012-0 (thread    4) identical     

007-0013-1 (thread    3) identical     

007-0014-0 (thread    1) identical     

007-0015-0 (thread    5) identical     

007-0016-1 (thread    2) identical     
007-0016-1 (thread    2) worse      

007-0017-1 (thread    6) identical     

007-0018-0 (thread    4) identical     

007-0019-1 (thread    3) identical     
007-0019-1 (thread    3) worse      

007-0020-1 (thread    5) identical     
007-0020-1 (thread    5) worse      

007-0021-0 (thread    2) identical     

007-0022-1 (thread    6) identical     

007-0023-0 (thread    1) identical     

007-0024-1 (thread    3) identical     

007-0025-0 (thread    4) identical     

007-0026-0 (thread    5) identical     

007-0027-1 (thread    2) identical     

007-0028-0 (thread    6) identical     

007-0029-0 (thread    3) identical     

007-0030-1 (thread    1) identical     

007-0031-1 (thread    4) identical     

007-0032-0 (thread    5) identical     

007-0033-1 (thread    2) identical     

007-0034-0 (thread    6) identical     
007-0034-0 (thread    6) worse      

007-0035-1 (thread    3) identical     
007-0035-1 (thread    3) worse      

007-0036-0 (thread    1) identical     
007-0036-0 (thread    1) worse      

007-0037-0 (thread    5) identical     

007-0038-1 (thread    4) identical     
007-0038-1 (thread    2) identical     
007-0038-1 (thread    4) worse      

007-0039-1 (thread    2) worse      

007-0040-0 (thread    6) identical     
007-0040-0 (thread    6) worse      

007-0041-1 (thread    3) identical     
007-0041-1 (thread    3) worse      

007-0042-1 (thread    2) identical     
007-0042-1 (thread    2) worse      

007-0043-0 (thread    1) identical     

007-0044-1 (thread    5) identical     
007-0044-1 (thread    5) worse      

007-0045-1 (thread    3) identical     
007-0045-1 (thread    3) worse      

007-0046-0 (thread    4) identical     

007-0047-0 (thread    2) identical     

007-0048-0 (thread    6) identical     

007-0049-1 (thread    1) identical     

007-0050-1 (thread    3) identical     
007-0050-1 (thread    3) worse      

007-0051-0 (thread    5) identical     
007-0051-0 (thread    5) worse      

007-0052-0 (thread    4) identical     
007-0052-0 (thread    4) worse      

007-0053-1 (thread    2) identical     

007-0054-0 (thread    6) identical     

007-0055-0 (thread    3) identical     

007-0056-1 (thread    1) identical     
007-0056-1 (thread    1) worse      

007-0057-1 (thread    5) identical     
007-0057-1 (thread    5) worse      

007-0058-0 (thread    4) identical     
007-0058-0 (thread    4) worse      

007-0059-1 (thread    2) identical     

007-0060-0 (thread    6) identical     
007-0060-0 (thread    6) worse      

007-0061-1 (thread    3) identical     

007-0062-0 (thread    1) identical     
007-0062-0 (thread    1) worse      

007-0063-1 (thread    5) identical     
007-0063-1 (thread    5) worse      

007-0064-0 (thread    4) identical     
007-0064-0 (thread    4) worse      

007-0065-0 (thread    6) identical     
007-0065-0 (thread    6) worse      

007-0066-1 (thread    2) identical     
007-0066-1 (thread    3) identical     
007-0066-1 (thread    2) worse      

007-0066-1 (thread    3) worse      

007-0068-1 (thread    1) identical     

Converged.

Converged2.
done
dvtditr (aa) Version 7.489
alg=A, model=BLOSUM62, 1.53, -0.00, -0.00, noshift, amax=0.0
6 thread(s)


Pairwise alignments were computed by FASTA
(Pearson & Lipman, 1988, PNAS 85:2444-2448)
Strategy:
 F-INS-i (Most accurate, but very slow)
 Iterative refinement method (<16) with LOCAL pairwise alignment information

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

Job Parameters:

Job parameter	Parameter value
datatype	`""`
cond_flavour	`{"__current_case__": 10, "dist_flavour": {"__current_case__": 4, "distance_method": "--fastapair", "weighti": "2.7"}, "fft": "true", "flavourType": "custom", "iterations": "1000", "score": "true"}`
ep	`"0.0"`
op	`"1.53"`
matrix_condition	`{"BLOSUM": "62", "__current_case__": 1, "matrix": "BLOSUM"}`
reorder	`"false"`
getTree	`"false"`
outputFormat	`"--clustalout"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"fasta"`

Passed s

✅ toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft (Test tool test #1)

Command Line:

Exit Code:

```
0
```

Standard Error:

nthread = 6
nthreadpair = 6
nthreadtb = 6
ppenalty_ex = 0
stacksize: -1 kb
rescale = 1
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 36 (thread    0)
done.

Constructing a UPGMA tree (efffree=0) ... 

    0 / 36
   10 / 36
   20 / 36
   30 / 36
done.

Progressive alignment 1/2... 

STEP     1 / 35 (thread    1) f��
STEP     3 / 35 (thread    5) f��
STEP     2 / 35 (thread    0) f��
STEP     4 / 35 (thread    2) f��
STEP     8 / 35 (thread    2) f��
STEP     7 / 35 (thread    1) f��
STEP     9 / 35 (thread    5) f��
STEP     5 / 35 (thread    3) f��
STEP    10 / 35 (thread    5) f��
STEP    11 / 35 (thread    0) f��
STEP     6 / 35 (thread    4) f��
STEP    12 / 35 (thread    5) f��
STEP    15 / 35 (thread    2) f��
STEP    16 / 35 (thread    2) f��
STEP    17 / 35 (thread    1) f��
STEP    18 / 35 (thread    2) f��
STEP    20 / 35 (thread    2) f��
STEP    19 / 35 (thread    1) f��
STEP    21 / 35 (thread    4) f��
STEP    22 / 35 (thread    3) f��
STEP    13 / 35 (thread    0) f��
STEP    24 / 35 (thread    4) f��
STEP    26 / 35 (thread    0) f��
STEP    14 / 35 (thread    5) f��
STEP    23 / 35 (thread    1) f��
STEP    25 / 35 (thread    2) f��
STEP    29 / 35 (thread    4) f��
STEP    30 / 35 (thread    0) f��
STEP    27 / 35 (thread    5) f��
STEP    31 / 35 (thread    1) f��
STEP    28 / 35 (thread    3) f��
STEP    32 / 35 (thread    2) f��
STEP    34 / 35 (thread    5) f��
STEP    33 / 35 (thread    4) f��
Reallocating..done. *alloclen = 2146

STEP    35 / 35 (thread    0) f��
done.

Making a distance matrix from msa.. 

    0 / 36 (thread    0)
done.

Constructing a UPGMA tree (efffree=1) ... 

    0 / 36
   10 / 36
   20 / 36
   30 / 36
done.

Progressive alignment 2/2... 

STEP     1 / 35 (thread    1) f��
STEP     2 / 35 (thread    2)
STEP     4 / 35 (thread    0) f�� f��
STEP     3 / 35 (thread    5) f��
STEP     6 / 35 (thread    3) f��
STEP     8 / 35 (thread    1) f��
STEP     9 / 35 (thread    2)
STEP     7 / 35 (thread    5) f�� f��
STEP    10 / 35 (thread    0) f��
STEP     5 / 35 (thread    4) f��
STEP    11 / 35 (thread    1) f��
STEP    12 / 35 (thread    2) f��
STEP    14 / 35 (thread    5) f��
STEP    16 / 35 (thread    2) f��
STEP    18 / 35 (thread    2) f��
STEP    17 / 35 (thread    5) f��
STEP    19 / 35 (thread    2) f��
STEP    20 / 35 (thread    5) f��
STEP    22 / 35 (thread    5) f��
STEP    24 / 35 (thread    3) f��
STEP    21 / 35 (thread    2) f��
STEP    23 / 35 (thread    5) f��
STEP    26 / 35 (thread    3) f��
STEP    28 / 35 (thread    4) f��
STEP    13 / 35 (thread    0) f��
STEP    29 / 35 (thread    3) f��
STEP    15 / 35 (thread    1) f��
STEP    25 / 35 (thread    2) f��
STEP    30 / 35 (thread    0) f��
STEP    31 / 35 (thread    1) f��
STEP    27 / 35 (thread    5) f��
STEP    32 / 35 (thread    3) f��
STEP    33 / 35 (thread    4) f��
STEP    34 / 35 (thread    2) f��
Reallocating..done. *alloclen = 2123

STEP    35 / 35 (thread    5) f��
done.

disttbfast (aa) Version 7.489
alg=A, model=BLOSUM62, 1.53, -0.00, -0.00, noshift, amax=0.0
6 thread(s)


Strategy:
 FFT-NS-2 (Fast but rough)
 Progressive method (guide trees were built 2 times.)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

Job Parameters:

Job parameter	Parameter value
datatype	`""`
cond_flavour	`{"__current_case__": 0, "flavourType": "mafft-fftns"}`
ep	`"0.0"`
op	`"1.53"`
matrix_condition	`{"BLOSUM": "62", "__current_case__": 1, "matrix": "BLOSUM"}`
reorder	`"false"`
getTree	`"false"`
outputFormat	`""`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"auto"`

✅ toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft (Test test against test.galaxyproject.org #2)

Command Line:

Exit Code:

```
0
```

Standard Error:

nthread = 6
nthreadpair = 6
nthreadtb = 6
ppenalty_ex = 0
stacksize: -1 kb
rescale = 1
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 36 (thread    0)
done.

Constructing a UPGMA tree (efffree=0) ... 

    0 / 36
   10 / 36
   20 / 36
   30 / 36
done.

Progressive alignment 1/2... 

STEP     1 / 35 (thread    0) d��
STEP     3 / 35 (thread    2)
STEP     2 / 35 (thread    1) d�� d��
STEP     4 / 35 (thread    4) d��
STEP     5 / 35 (thread    3) d��
STEP     8 / 35 (thread    1) d��
STEP     6 / 35 (thread    5) d��
STEP     9 / 35 (thread    1) d��
STEP    10 / 35 (thread    2) d��
STEP     7 / 35 (thread    4) d��
STEP    11 / 35 (thread    1) d��
STEP    12 / 35 (thread    2) d��
STEP    15 / 35 (thread    3) d��
STEP    13 / 35 (thread    1) d��
STEP    16 / 35 (thread    0) d��
STEP    17 / 35 (thread    5) d��
STEP    20 / 35 (thread    3) d��
STEP    18 / 35 (thread    0) d��
STEP    21 / 35 (thread    1) d��
STEP    14 / 35 (thread    2) d��
STEP    22 / 35 (thread    5) d��
STEP    19 / 35 (thread    4) d��
STEP    26 / 35 (thread    1) d��
STEP    23 / 35 (thread    5) d��
STEP    24 / 35 (thread    0) d��
STEP    30 / 35 (thread    0) d��
STEP    25 / 35 (thread    3) d��
STEP    29 / 35 (thread    5) d��
STEP    27 / 35 (thread    2) d��
STEP    32 / 35 (thread    3) d��
STEP    31 / 35 (thread    1) d��
STEP    28 / 35 (thread    4) d��
STEP    33 / 35 (thread    0) d��
STEP    34 / 35 (thread    5) d��
Reallocating..done. *alloclen = 2146

STEP    35 / 35 (thread    2) d�� h
done.

Making a distance matrix from msa.. 

    0 / 36 (thread    0)
done.

Constructing a UPGMA tree (efffree=1) ... 

    0 / 36
   10 / 36
   20 / 36
   30 / 36
done.

Progressive alignment 2/2... 

STEP     1 / 35 (thread    0) d��
STEP     2 / 35 (thread    1) d��
STEP     3 / 35 (thread    2) d��
STEP     4 / 35 (thread    4) d��
STEP     5 / 35 (thread    3) d��
STEP     8 / 35 (thread    2) d��
STEP     6 / 35 (thread    5) d��
STEP     9 / 35 (thread    1) d��
STEP     7 / 35 (thread    4) d��
STEP    10 / 35 (thread    0) d��
STEP    11 / 35 (thread    2) d��
STEP    12 / 35 (thread    1) d��
STEP    13 / 35 (thread    3) d��
STEP    14 / 35 (thread    0) d��
STEP    16 / 35 (thread    5) d��
STEP    18 / 35 (thread    1) d��
STEP    19 / 35 (thread    0) d��
STEP    20 / 35 (thread    1) d��
STEP    21 / 35 (thread    5) d��
STEP    17 / 35 (thread    4) d��
STEP    22 / 35 (thread    3) d��
STEP    15 / 35 (thread    2) d��
STEP    24 / 35 (thread    4) d��
STEP    25 / 35 (thread    1) d��
STEP    23 / 35 (thread    0) d��
STEP    29 / 35 (thread    4) d��
STEP    26 / 35 (thread    3) d��
STEP    28 / 35 (thread    5) d��
STEP    27 / 35 (thread    2) d��
STEP    30 / 35 (thread    1) d��
STEP    31 / 35 (thread    0) d��
STEP    33 / 35 (thread    4) d��
STEP    32 / 35 (thread    3) d��
STEP    34 / 35 (thread    5) d��
Reallocating..done. *alloclen = 2123

STEP    35 / 35 (thread    2) d�� h
done.

disttbfast (aa) Version 7.489
alg=A, model=BLOSUM62, 1.53, -0.00, -0.00, noshift, amax=0.0
6 thread(s)


Strategy:
 NW-NS-2 (Fast but rough)
 Progressive method (guide trees were built 2 times.)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

Job Parameters:

Job parameter	Parameter value
datatype	`""`
cond_flavour	`{"__current_case__": 3, "flavourType": "mafft-nwns"}`
ep	`"0.0"`
op	`"1.53"`
matrix_condition	`{"BLOSUM": "62", "__current_case__": 1, "matrix": "BLOSUM"}`
reorder	`"false"`
getTree	`"false"`
outputFormat	`"--clustalout"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"fasta"`

jennaj · 2022-02-25T23:27:06Z

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.489+galaxy0

mvdbeek · 2022-02-25T23:29:06Z

Results (powered by Planemo)

Summary

State	Count
Total	3
Passed	2
Error	0
Failure	1
Skipped	0

Failed s

❌ toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft (Test Test Prokka 1.14.6+galaxy1 #3)

Problems:

Output outputAlignment:  different than expected, difference (using diff):
( /tmp/tmplrzwegxqmafft_custom_result.aln v. /tmp/tmppd_e491umafft_custom_result.aln )
--- local_file
+++ history_data
@@ -1,233 +1,233 @@
-CLUSTAL format alignment by MAFFT F-INS-i (v7.455)
-
-
-1==             MN------------------------GTE--GDNFYVPFS--------NKTGL-ARSPYE
-2==             MN------------------------GTE--GPNFYVPFS--------NITGV-VRSPFE
-3==             MN------------------------GTE--GINFYVPMS--------NKTGV-VRSPFE
-4=p             MN------------------------GTE--GKNFYVPMS--------NRTGL-VRSPFE
-5=p             MN------------------------GTE--GNNFYVPLS--------NRTGL-VRSPFE
-6==             MK------------------------QVPEFHEDFYIPIP-------LDINNLSAYSPFL
-7==             MR------------------------KMS--EEEFYL------------FKNISSVGPWD
-8=opsin,        ------------------------------------------------------------
-9==             MAQQWSLQ-RLAGRHPQDS----YEDSTQ--SSIFTYTNS--------NS----TRGPFE
-10==            MAQQWSLQ-RLAGRHPQDS----YEDSTQ--SSIFTYTNS--------NS----TRGPFE
-11==            MTEAWNVAVFAARRSRDD------DDTTR--GSVFTYTNT--------NN----TRGPFE
-12==            MA-AWEAA-FAARRRHEE------EDTTR--DSVFTYTNS--------NN----TRGPFE
-13==            MS----------------------SNSSQ--------------AP--PNG----TPGPFD
-14==            MESG-NV-----------------------------------------SSSLFGNVSTAL
-15==            MEYH-NV------------------------------------------SSVLGNVSSVL
-16==            MEPLCNA------------------------------------------------SEPPL
-17==            MDALCNA------------------------------------------------SEPPL
-18==            MT-------------------------------------------------------NAT
-19==            MA-------------------------------------------------------NVT
********
*SNIP *
********
+13==            -------------------------------------------PV
+14==            ---------------------------------------------
+15==            ---------------------------------------------
+16==            ---------------------------------------------
+17==            ---------------------------------------------
+18==            ---------------------------------------------
+19==            ---------------------------------------------
+20==            ---------------------------------------------
+21==            ---------------------------------------------
+22==            ---------------------------------------------
+23==            ---------------------------------------------
+24==            ---------------------------------------------
+25==            ---------------------------------------------
+26==            ---------------------------------------------
+27==            QGYPPQGYPPQGYPPQGYPPQGAPPQVEAPQGAPPQGVDNQAYQA
+28==            QGYPPQGYPPQGYPP---PPQGAPPQ-GAPPAAPPQGVDNQAYQA
+29==            -----------------------------------DYCRKKGHDS
+30==            -----------------------------------DHCGKKGHDT
+31=p            -----------------------------------DHCGKKGHDT
+32==            ---------------------------------------------
+33=p            ---------------------------------------------
+34==            ---------------------------------------------
+35=p            ---------------------------------------------
+36==            ------------------------PQ-------------------
+

Command Line:

Exit Code:

```
0
```

Standard Error:

rescale = 1
query :    1 /    36
query :    2 /    36
query :    3 /    36
query :    4 /    36
query :    5 /    36
query :    6 /    36
query :    7 /    36
query :    8 /    36
query :    9 /    36
query :   10 /    36
query :   11 /    36
query :   12 /    36
query :   13 /    36
query :   14 /    36
query :   15 /    36
query :   16 /    36
query :   17 /    36
query :   18 /    36
query :   19 /    36
query :   20 /    36
query :   21 /    36
query :   22 /    36
query :   23 /    36
query :   24 /    36
query :   25 /    36
query :   26 /    36
query :   27 /    36
query :   28 /    36
query :   29 /    36
query :   30 /    36
query :   31 /    36
query :   32 /    36
query :   33 /    36
query :   34 /    36
query :   35 /    36
query :   36 /    36
##### writing hat3
dndfast7 (aa) Version 7.489
alg=, model=BLOSUM62, -0.00, -0.00, -0.00, noshift, amax=0.0
1 thread(s)

treein = 0
compacttree = 0
stacksize: -1 kb
Loading 'hat3' ... 
done.
rescale = 1
Gap Penalty = -1.53, +0.00, +0.00
tbutree = 1, compacttree = 0
Loading 'hat2' ... done.
Constructing a UPGMA tree ... 

    0 / 36
   10 / 36
   20 / 36
   30 / 36
done.

Progressive alignment ... 

STEP     1 /35 (thread    2) 
STEP     2 /35 (thread    1) 
STEP     3 /35 (thread    0) 
STEP     5 /35 (thread    3) 
STEP     7 /35 (thread    0) 
STEP     4 /35 (thread    4) 
STEP     8 /35 (thread    0) 
STEP     9 /35 (thread    3) 
STEP    10 /35 (thread    1) 
STEP     6 /35 (thread    5) 
STEP    12 /35 (thread    3) 
STEP    14 /35 (thread    4) 
STEP    11 /35 (thread    0) 
STEP    15 /35 (thread    3) 
STEP    17 /35 (thread    0) 
STEP    13 /35 (thread    1) 
STEP    18 /35 (thread    2) 
STEP    19 /35 (thread    3) 
STEP    16 /35 (thread    4) 
STEP    20 /35 (thread    5) 
STEP    21 /35 (thread    1) 
STEP    23 /35 (thread    4) 
STEP    24 /35 (thread    5) 
STEP    22 /35 (thread    0) 
STEP    26 /35 (thread    2) 
STEP    27 /35 (thread    5) 
STEP    31 /35 (thread    0) 
STEP    25 /35 (thread    3) 
STEP    28 /35 (thread    1) 
STEP    29 /35 (thread    4) 
STEP    32 /35 (thread    3) 
STEP    30 /35 (thread    2) 
STEP    34 /35 (thread    1) 
STEP    33 /35 (thread    5) 
Reallocating (by thread 0) ..done. *alloclen = 2122

STEP    35 /35 (thread    0) 
done.
tbfast (aa) Version 7.489
alg=A, model=BLOSUM62, 1.53, -0.00, -0.00, noshift, amax=0.0
6 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 6
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 16
sueff_global = 0.100000
nadd = 16
Loading 'hat3' ... done.
rescale = 1


    0 / 36
   10 / 36
   20 / 36
   30 / 36
Segment   1/  1    1- 714
001-0000-0 (thread    3) identical     

001-0000-1 (thread    4) identical     

001-0002-1 (thread    6) identical     

001-0003-1 (thread    2) identical     

001-0004-0 (thread    1) identical     

001-0005-0 (thread    5) identical     

001-0006-1 (thread    4) identical     

001-0007-0 (thread    6) identical     

001-0008-1 (thread    2) identical     

001-0009-0 (thread    1) identical     
001-0009-0 (thread    1) better     

001-0010-1 (thread    6) identical     

001-0011-0 (thread    4) identical     

001-0012-1 (thread    5) identical     

001-0013-0 (thread    2) identical     

001-0014-1 (thread    1) identical     
001-0014-1 (thread    1) worse      

001-0015-0 (thread    3) identical     

001-0016-0 (thread    6) identical     

001-0017-1 (thread    4) identical     

001-0018-1 (thread    2) identical     
001-0018-1 (thread    2) worse      

001-0019-1 (thread    3) identical     

001-0020-0 (thread    5) identical     

001-0021-0 (thread    1) identical     

001-0021-0 (thread    6) identical     

001-0023-1 (thread    4) identical     

001-0024-1 (thread    3) identical     

001-0025-0 (thread    5) identical     

001-0026-0 (thread    2) identical     

001-0027-0 (thread    6) identical     

001-0028-1 (thread    1) identical     

001-0029-1 (thread    4) identical     

001-0030-0 (thread    2) identical     

001-0031-1 (thread    6) identical     

001-0032-0 (thread    3) identical     

001-0033-1 (thread    5) identical     

001-0034-0 (thread    1) identical     

001-0035-0 (thread    3) identical     

001-0036-1 (thread    4) identical     
001-0036-1 (thread    4) worse      

001-0037-1 (thread    5) identical     
001-0037-0 (thread    1) identical     
001-0037-1 (thread    5) worse      

001-0038-0 (thread    1) worse      

001-0039-0 (thread    2) identical     
001-0039-1 (thread    6) identical     
001-0039-0 (thread    2) worse      

001-0040-1 (thread    6) worse      

001-0041-1 (thread    3) identical     
001-0041-1 (thread    3) worse      

001-0042-1 (thread    2) identical     
001-0042-1 (thread    2) worse      

001-0043-0 (thread    4) identical     

001-0044-1 (thread    5) identical     
001-0044-1 (thread    5) worse      

001-0045-0 (thread    2) identical     

001-0046-0 (thread    1) identical     
001-0046-1 (thread    3) identical     
001-0046-1 (thread    3) worse      
001-0046-0 (thread    1) better     


001-0048-0 (thread    6) identical     

001-0049-1 (thread    4) identical     

001-0050-1 (thread    2) identical     

001-0051-0 (thread    6) identical     
001-0051-0 (thread    6) worse      

001-0052-0 (thread    1) identical     
001-0052-1 (thread    3) identical     
001-0052-0 (thread    1) worse      

001-0053-1 (thread    3) worse      

001-0054-0 (thread    5) identical     

001-0055-0 (thread    2) identical     
001-0055-1 (thread    4) identical     

001-0056-0 (thread    2) worse      

001-0057-1 (thread    6) identical     
001-0057-1 (thread    6) worse      

001-0058-0 (thread    1) identical     
001-0058-0 (thread    1) worse      

001-0059-0 (thread    5) identical     
001-0059-0 (thread    5) worse      

001-0060-1 (thread    3) identical     
001-0060-1 (thread    3) worse      

001-0061-1 (thread    4) identical     
001-0061-1 (thread    4) better     

001-0062-1 (thread    6) identical     
001-0062-1 (thread    6) better     

001-0063-0 (thread    2) identical     
001-0063-0 (thread    2) better     

001-0064-1 (thread    6) identical     
001-0064-1 (thread    6) worse      

001-0065-0 (thread    3) identical     
001-0065-0 (thread    3) better     

001-0066-1 (thread    5) identical     
001-0066-1 (thread    5) worse      

001-0067-1 (thread    4) identical     
001-0067-1 (thread    4) better     

001-0068-0 (thread    1) identical     
001-0068-0 (thread    1) worse      

002-0000-1 (thread    4) identical     

002-0001-0 (thread    5) identical     

002-0002-0 (thread    6) identical     

002-0003-0 (thread    3) identical     

002-0004-1 (thread    4) identical     

002-0005-1 (thread    2) identical     

002-0006-0 (thread    6) identical     

002-0007-0 (thread    4) identical     

002-0008-1 (thread    3) identical     

002-0009-0 (thread    5) identical     

002-0010-1 (thread    4) identical     

002-0011-0 (thread    6) identical     

002-0012-1 (thread    2) identical     

002-0013-0 (thread    4) identical     

002-0014-0 (thread    3) identical     

002-0002-1 (thread    1) identical     

002-0016-1 (thread    5) identical     
002-0016-1 (thread    5) worse      

002-0017-1 (thread    6) identical     

002-0018-1 (thread    4) identical     
002-0018-1 (thread    4) worse      

002-0019-1 (thread    1) identical     

002-0020-0 (thread    5) identical     

002-0021-1 (thread    6) identical     

002-0022-0 (thread    3) identical     
002-0022-0 (thread    3) better     

002-0023-1 (thread    1) identical     

002-0024-0 (thread    4) identical     

002-0025-1 (thread    6) identical     

002-0026-0 (thread    3) identical     

002-0027-0 (thread    5) identical     

002-0028-0 (thread    4) identical     

002-0029-1 (thread    6) identical     

002-0030-0 (thread    3) identical     

002-0031-1 (thread    5) identical     

002-0032-0 (thread    2) identical     

002-0033-0 (thread    4) identical     

002-0034-1 (thread    6) identical     
002-0034-0 (thread    2) identical     

002-0035-1 (thread    6) worse      

002-0036-1 (thread    4) identical     
002-0036-1 (thread    4) worse      

002-0037-0 (thread    3) identical     
002-0037-0 (thread    3) worse      

002-0038-1 (thread    5) identical     
002-0038-1 (thread    5) worse      

002-0039-1 (thread    6) identical     
002-0039-1 (thread    6) worse      

002-0040-0 (thread    4) identical     

002-0041-1 (thread    1) identical     

002-0042-1 (thread    3) identical     
002-0042-1 (thread    3) worse      

002-0043-1 (thread    6) identical     
002-0043-1 (thread    6) worse      

002-0044-0 (thread    5) identical     

002-0045-1 (thread    1) identical     
002-0045-1 (thread    1) worse      

002-0046-0 (thread    3) identical     

002-0047-0 (thread    2) identical     
002-0047-0 (thread    2) worse      

002-0048-0 (thread    4) identical     
002-0048-0 (thread    4) worse      

002-0049-1 (thread    6) identical     

002-0050-0 (thread    5) identical     

002-0051-1 (thread    2) identical     
002-0051-0 (thread    3) identical     
002-0051-1 (thread    2) better     

002-0051-0 (thread    3) worse      

002-0053-1 (thread    1) identical     

002-0054-0 (thread    4) identical     
002-0054-0 (thread    4) worse      

002-0055-1 (thread    3) identical     
002-0055-1 (thread    3) worse      

002-0056-1 (thread    6) identical     

002-0057-0 (thread    2) identical     
002-0057-0 (thread    2) better     

002-0058-1 (thread    3) identical     
002-0058-1 (thread    3) worse      

002-0059-0 (thread    4) identical     
002-0059-0 (thread    4) worse      

002-0060-0 (thread    6) identical     

002-0061-0 (thread    5) identical     
002-0061-1 (thread    2) identical     
002-0061-1 (thread    2) better     

002-0062-0 (thread    5) worse      

002-0063-0 (thread    6) identical     
002-0063-0 (thread    6) better     

002-0064-1 (thread    1) identical     
002-0064-1 (thread    1) worse      

002-0065-1 (thread    2) identical     
002-0065-0 (thread    3) identical     
002-0065-1 (thread    2) worse      

002-0066-0 (thread    3) worse      

002-0067-1 (thread    5) identical     
002-0067-1 (thread    5) worse      

002-0068-1 (thread    4) identical     
002-0068-1 (thread    4) better     

003-0000-1 (thread    1) identical     

003-0001-1 (thread    6) identical     

003-0002-0 (thread    5) identical     

003-0003-0 (thread    4) identical     

003-0004-0 (thread    2) identical     
003-0004-1 (thread    3) identical     


003-0006-1 (thread    6) identical     

003-0007-0 (thread    1) identical     

003-0008-0 (thread    5) identical     

003-0009-1 (thread    4) identical     

003-0010-0 (thread    3) identical     
003-0010-0 (thread    3) worse      

003-0011-1 (thread    2) identical     

003-0012-0 (thread    6) identical     

003-0013-1 (thread    1) identical     

003-0014-0 (thread    5) identical     
003-0014-0 (thread    3) identical     

003-0014-0 (thread    5) worse      

003-0016-1 (thread    4) identical     
003-0016-1 (thread    4) worse      

003-0017-0 (thread    6) identical     

003-0018-1 (thread    2) identical     

003-0019-1 (thread    1) identical     

003-0020-0 (thread    4) identical     

003-0021-1 (thread    6) identical     

003-0022-1 (thread    5) identical     

003-0023-1 (thread    1) identical     

003-0024-0 (thread    3) identical     

003-0025-0 (thread    2) identical     

003-0026-1 (thread    6) identical     

003-0027-0 (thread    4) identical     

003-0028-1 (thread    1) identical     

003-0029-0 (thread    5) identical     

003-0030-0 (thread    3) identical     

003-0031-0 (thread    6) identical     

003-0032-1 (thread    2) identical     

003-0033-1 (thread    4) identical     

003-0034-0 (thread    1) identical     
003-0034-0 (thread    1) worse      

003-0035-1 (thread    5) identical     
003-0035-1 (thread    5) worse      

003-0036-1 (thread    6) identical     
003-0036-1 (thread    6) worse      

003-0037-0 (thread    1) identical     
003-0037-0 (thread    2) identical     

003-0038-0 (thread    1) worse      

003-0039-0 (thread    3) identical     
003-0039-0 (thread    3) better     

003-0040-1 (thread    4) identical     
003-0040-1 (thread    4) better     

003-0041-0 (thread    6) identical     

003-0042-1 (thread    3) identical     
003-0042-1 (thread    5) identical     
003-0042-1 (thread    3) worse      

003-0043-1 (thread    5) worse      

003-0044-1 (thread    2) identical     
003-0044-1 (thread    2) worse      

003-0045-0 (thread    1) identical     
003-0045-0 (thread    1) better     

003-0046-0 (thread    3) identical     

003-0047-1 (thread    6) identical     
003-0047-1 (thread    6) worse      

003-0048-1 (thread    1) identical     
003-0048-1 (thread    1) worse      

003-0049-1 (thread    5) identical     

003-0050-0 (thread    4) identical     

003-0051-0 (thread    2) identical     
003-0051-0 (thread    2) worse      

003-0052-1 (thread    6) identical     

003-0053-0 (thread    3) identical     
003-0053-0 (thread    3) better     

003-0054-0 (thread    1) identical     
003-0054-0 (thread    1) better     

003-0055-0 (thread    1) identical     
003-0055-0 (thread    1) better     

003-0056-0 (thread    6) identical     
003-0056-1 (thread    1) identical     
003-0056-1 (thread    1) worse      

003-0057-0 (thread    6) worse      

003-0058-1 (thread    2) identical     
003-0058-1 (thread    2) better     

003-0059-0 (thread    1) identical     
003-0059-1 (thread    6) identical     
003-0059-0 (thread    1) better     

003-0059-1 (thread    6) worse      

003-0061-0 (thread    6) identical     
003-0061-0 (thread    6) better     

003-0062-1 (thread    6) identical     
003-0062-1 (thread    6) worse      

003-0063-1 (thread    5) identical     
003-0063-0 (thread    4) identical     

003-0063-1 (thread    5) better     

003-0065-0 (thread    2) identical     
003-0065-0 (thread    2) worse      

003-0066-1 (thread    3) identical     

003-0067-1 (thread    6) identical     
003-0067-1 (thread    1) identical     

003-0068-1 (thread    6) worse      

004-0000-0 (thread    1) identical     

004-0001-0 (thread    2) identical     

004-0002-1 (thread    3) identical     

004-0003-0 (thread    4) identical     

004-0004-1 (thread    5) identical     

004-0005-1 (thread    6) identical     

004-0006-0 (thread    1) identical     

004-0007-1 (thread    2) identical     

004-0008-0 (thread    3) identical     

004-0009-1 (thread    4) identical     

004-0010-0 (thread    5) identical     
004-0010-1 (thread    6) identical     

004-0011-0 (thread    5) worse      

004-0012-0 (thread    1) identical     

004-0013-1 (thread    2) identical     

004-0014-0 (thread    6) identical     

004-0015-0 (thread    3) identical     

004-0016-0 (thread    1) identical     

004-0017-1 (thread    4) identical     

004-0018-1 (thread    5) identical     

004-0019-1 (thread    2) identical     

004-0020-0 (thread    1) identical     

004-0021-0 (thread    6) identical     

004-0022-1 (thread    3) identical     

004-0023-1 (thread    4) identical     

004-0024-0 (thread    5) identical     

004-0025-0 (thread    1) identical     

004-0026-1 (thread    6) identical     

004-0027-1 (thread    2) identical     

004-0028-0 (thread    3) identical     

004-0029-1 (thread    4) identical     

004-0030-0 (thread    6) identical     

004-0031-1 (thread    2) identical     

004-0032-0 (thread    5) identical     

004-0033-1 (thread    1) identical     
004-0033-1 (thread    1) worse      

004-0034-0 (thread    3) identical     

004-0035-1 (thread    4) identical     
004-0035-1 (thread    4) worse      

004-0036-1 (thread    1) identical     
004-0036-0 (thread    6) identical     

004-0037-1 (thread    1) worse      

004-0038-0 (thread    5) identical     

004-0039-0 (thread    3) identical     
004-0039-0 (thread    3) worse      

004-0040-1 (thread    2) identical     
004-0040-1 (thread    2) worse      

004-0041-1 (thread    4) identical     
004-0041-1 (thread    4) worse      

004-0042-1 (thread    1) identical     
004-0042-0 (thread    6) identical     

004-0043-1 (thread    1) worse      

004-0044-1 (thread    3) identical     
004-0044-1 (thread    3) worse      

004-0045-0 (thread    6) identical     

004-0046-1 (thread    4) identical     
004-0046-1 (thread    4) worse      

004-0047-0 (thread    5) identical     

004-0048-1 (thread    1) identical     

004-0049-0 (thread    2) identical     

004-0050-1 (thread    6) identical     
004-0050-1 (thread    6) worse      

004-0051-0 (thread    3) identical     

004-0052-0 (thread    4) identical     

004-0053-1 (thread    5) identical     
004-0053-1 (thread    5) better     

004-0054-0 (thread    1) identical     
004-0054-0 (thread    1) worse      

004-0055-1 (thread    3) identical     
004-0055-1 (thread    3) better     

004-0056-0 (thread    1) identical     
004-0056-0 (thread    1) worse      

004-0057-0 (thread    6) identical     
004-0057-0 (thread    4) identical     
004-0057-0 (thread    6) better     

004-0057-1 (thread    3) identical     
004-0058-1 (thread    3) worse      

004-0059-0 (thread    4) worse      

004-0060-0 (thread    1) identical     
004-0060-0 (thread    1) better     

004-0061-1 (thread    6) identical     
004-0061-0 (thread    1) identical     
004-0061-1 (thread    6) better     

004-0062-0 (thread    1) worse      

004-0063-1 (thread    6) identical     
004-0063-1 (thread    2) identical     

004-0064-1 (thread    6) worse      

004-0065-0 (thread    3) identical     
004-0065-1 (thread    1) identical     
004-0065-1 (thread    1) worse      

004-0066-0 (thread    3) worse      

004-0067-1 (thread    4) identical     
004-0067-1 (thread    5) identical     

004-0068-1 (thread    4) worse      

005-0000-0 (thread    1) identical     

005-0001-1 (thread    6) identical     

005-0002-1 (thread    4) identical     

005-0003-0 (thread    5) identical     

005-0004-1 (thread    3) identical     

005-0005-0 (thread    2) identical     

005-0006-1 (thread    6) identical     

005-0007-0 (thread    1) identical     

005-0008-0 (thread    4) identical     

005-0009-0 (thread    3) identical     
005-0009-0 (thread    3) worse      

005-0010-1 (thread    5) identical     

005-0011-1 (thread    2) identical     
005-0011-1 (thread    2) worse      

005-0012-0 (thread    6) identical     

005-0013-1 (thread    1) identical     

005-0014-0 (thread    4) identical     

005-0015-0 (thread    5) identical     

005-0016-1 (thread    3) identical     

005-0017-1 (thread    2) identical     

005-0018-0 (thread    6) identical     

005-0019-1 (thread    1) identical     

005-0020-1 (thread    5) identical     

005-0021-0 (thread    3) identical     

005-0022-1 (thread    2) identical     

005-0023-0 (thread    4) identical     

005-0024-1 (thread    1) identical     

005-0025-0 (thread    6) identical     

005-0026-0 (thread    5) identical     

005-0027-1 (thread    3) identical     

005-0028-0 (thread    2) identical     

005-0029-1 (thread    4) identical     

005-0030-0 (thread    1) identical     

005-0031-1 (thread    6) identical     
005-0031-1 (thread    6) worse      

005-0032-0 (thread    5) identical     

005-0033-1 (thread    3) identical     

005-0034-0 (thread    2) identical     

005-0035-1 (thread    4) identical     
005-0035-1 (thread    4) worse      

005-0036-0 (thread    1) identical     
005-0036-0 (thread    1) better     

005-0037-0 (thread    2) identical     
005-0037-0 (thread    2) worse      

005-0038-1 (thread    3) identical     
005-0038-0 (thread    5) identical     

005-0039-1 (thread    3) worse      

005-0040-1 (thread    4) identical     
005-0040-1 (thread    4) worse      

005-0041-0 (thread    1) identical     

005-0042-1 (thread    6) identical     
005-0042-1 (thread    6) worse      

005-0043-1 (thread    3) identical     
005-0043-1 (thread    3) better     

005-0044-0 (thread    6) identical     

005-0045-1 (thread    1) identical     
005-0045-1 (thread    1) worse      

005-0046-1 (thread    2) identical     
005-0046-1 (thread    2) worse      

005-0047-0 (thread    5) identical     

005-0048-1 (thread    3) identical     

005-0049-0 (thread    4) identical     

005-0050-1 (thread    1) identical     
005-0050-1 (thread    1) better     

005-0051-0 (thread    3) identical     
005-0051-0 (thread    3) worse      

005-0052-0 (thread    6) identical     

005-0053-1 (thread    5) identical     

005-0054-0 (thread    2) identical     

005-0055-0 (thread    1) identical     

005-0056-1 (thread    4) identical     

005-0057-0 (thread    6) identical     
005-0057-1 (thread    3) identical     

005-0057-0 (thread    6) worse      

005-0059-1 (thread    1) identical     
005-0059-0 (thread    2) identical     
005-0059-1 (thread    1) better     

005-0060-0 (thread    2) worse      

005-0061-0 (thread    4) identical     
005-0061-0 (thread    4) better     

005-0062-0 (thread    6) identical     
005-0062-0 (thread    6) worse      

005-0063-1 (thread    3) identical     
005-0063-1 (thread    3) better     

005-0064-1 (thread    5) identical     

005-0065-0 (thread    2) identical     
005-0065-0 (thread    2) better     

005-0066-1 (thread    4) identical     

005-0067-1 (thread    6) identical     
005-0067-1 (thread    6) worse      

005-0068-1 (thread    1) identical     
005-0068-1 (thread    1) worse      

006-0000-0 (thread    6) identical     

006-0001-1 (thread    2) identical     

006-0002-0 (thread    3) identical     

006-0002-1 (thread    5) identical     

006-0004-0 (thread    6) identical     

006-0005-0 (thread    2) identical     

006-0006-1 (thread    1) identical     

006-0007-0 (thread    2) identical     
006-0007-0 (thread    2) worse      

006-0008-1 (thread    3) identical     

006-0009-0 (thread    5) identical     

006-0010-1 (thread    6) identical     

006-0011-0 (thread    2) identical     

006-0012-1 (thread    3) identical     

006-0013-0 (thread    6) identical     

006-0014-0 (thread    4) identical     

006-0015-1 (thread    2) identical     
006-0015-1 (thread    2) worse      

006-0016-1 (thread    5) identical     
006-0016-1 (thread    5) worse      

006-0017-1 (thread    2) identical     

006-0018-1 (thread    6) identical     

006-0019-0 (thread    3) identical     

006-0020-0 (thread    5) identical     

006-0021-0 (thread    4) identical     

006-0022-1 (thread    2) identical     

006-0023-1 (thread    3) identical     

006-0024-0 (thread    5) identical     

006-0025-1 (thread    1) identical     
006-0025-0 (thread    6) identical     

006-0026-1 (thread    1) worse      

006-0027-0 (thread    2) identical     

006-0028-0 (thread    5) identical     

006-0029-1 (thread    3) identical     

006-0030-0 (thread    1) identical     

006-0031-1 (thread    6) identical     
006-0031-1 (thread    6) worse      

006-0032-1 (thread    2) identical     

006-0033-0 (thread    5) identical     

006-0034-1 (thread    5) identical     
006-0034-1 (thread    5) worse      

006-0035-1 (thread    3) identical     
006-0035-1 (thread    3) worse      

006-0036-0 (thread    2) identical     

006-0037-1 (thread    6) identical     
006-0037-1 (thread    6) worse      

006-0038-0 (thread    5) identical     
006-0038-0 (thread    5) worse      

006-0039-1 (thread    4) identical     

006-0040-1 (thread    3) identical     
006-0040-1 (thread    3) worse      

006-0041-0 (thread    2) identical     

006-0042-1 (thread    4) identical     
006-0042-1 (thread    4) better     

006-0042-1 (thread    2) identical     
006-0042-1 (thread    2) worse      

006-0043-1 (thread    6) identical     
006-0043-1 (thread    6) worse      

006-0044-0 (thread    1) identical     
006-0044-0 (thread    2) identical     

006-0045-0 (thread    1) worse      

006-0046-0 (thread    5) identical     

006-0048-0 (thread    3) identical     

006-0049-1 (thread    6) identical     

006-0050-0 (thread    2) identical     
006-0050-0 (thread    5) identical     
006-0050-0 (thread    2) worse      

006-0051-0 (thread    5) worse      

006-0052-0 (thread    3) identical     
006-0052-0 (thread    3) worse      

006-0053-1 (thread    5) identical     
006-0053-1 (thread    5) worse      

006-0054-1 (thread    1) identical     
006-0054-1 (thread    1) worse      

006-0055-0 (thread    2) identical     

006-0056-1 (thread    6) identical     

006-0057-1 (thread    4) identical     

006-0058-1 (thread    2) identical     
006-0058-1 (thread    2) better     

006-0059-0 (thread    2) identical     
006-0059-0 (thread    2) worse      

006-0060-0 (thread    3) identical     
006-0060-0 (thread    3) worse      

006-0061-0 (thread    6) identical     
006-0061-0 (thread    6) better     

006-0062-1 (thread    2) identical     
006-0062-1 (thread    2) worse      

006-0063-1 (thread    6) identical     
006-0063-1 (thread    6) worse      

006-0064-1 (thread    5) identical     

006-0065-0 (thread    1) identical     
006-0065-0 (thread    1) worse      

006-0066-0 (thread    3) identical     
006-0066-0 (thread    3) worse      

006-0067-1 (thread    4) identical     
006-0067-1 (thread    4) worse      

006-0068-1 (thread    2) identical     
006-0068-1 (thread    2) worse      

Converged2.
done
dvtditr (aa) Version 7.489
alg=A, model=BLOSUM62, 1.53, -0.00, -0.00, noshift, amax=0.0
6 thread(s)


Pairwise alignments were computed by FASTA
(Pearson & Lipman, 1988, PNAS 85:2444-2448)
Strategy:
 F-INS-i (Most accurate, but very slow)
 Iterative refinement method (<16) with LOCAL pairwise alignment information

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

Job Parameters:

Job parameter	Parameter value
datatype	`""`
cond_flavour	`{"__current_case__": 10, "dist_flavour": {"__current_case__": 4, "distance_method": "--fastapair", "weighti": "2.7"}, "fft": "true", "flavourType": "custom", "iterations": "1000", "score": "true"}`
ep	`"0.0"`
op	`"1.53"`
matrix_condition	`{"BLOSUM": "62", "__current_case__": 1, "matrix": "BLOSUM"}`
reorder	`"false"`
getTree	`"false"`
outputFormat	`"--clustalout"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"fasta"`

Passed s

✅ toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft (Test tool test #1)

Command Line:

Exit Code:

```
0
```

Standard Error:

nthread = 6
nthreadpair = 6
nthreadtb = 6
ppenalty_ex = 0
stacksize: -1 kb
rescale = 1
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 36 (thread    0)
done.

Constructing a UPGMA tree (efffree=0) ... 

    0 / 36
   10 / 36
   20 / 36
   30 / 36
done.

Progressive alignment 1/2... 

STEP     1 / 35 (thread    0)
STEP     2 / 35 (thread    1) f��
STEP     3 / 35 (thread    2) f��
STEP     4 / 35 (thread    3) f�� f��
STEP     5 / 35 (thread    4) f��
STEP     8 / 35 (thread    2) f��
STEP     7 / 35 (thread    3) f��
STEP     9 / 35 (thread    1) f��
STEP    10 / 35 (thread    0) f��
STEP    11 / 35 (thread    2) f��
STEP     6 / 35 (thread    5) f��
STEP    12 / 35 (thread    0) f��
STEP    15 / 35 (thread    0) f��
STEP    13 / 35 (thread    1) f��
STEP    16 / 35 (thread    4) f��
STEP    17 / 35 (thread    0) f��
STEP    18 / 35 (thread    5) f��
STEP    20 / 35 (thread    0) f��
STEP    21 / 35 (thread    5) f��
STEP    19 / 35 (thread    3) f��
STEP    22 / 35 (thread    5) f��
STEP    14 / 35 (thread    2) f��
STEP    24 / 35 (thread    1) f��
STEP    26 / 35 (thread    0) f��
STEP    23 / 35 (thread    4) f��
STEP    29 / 35 (thread    0) f��
STEP    25 / 35 (thread    3) f��
STEP    30 / 35 (thread    1) f��
STEP    27 / 35 (thread    2) f��
STEP    31 / 35 (thread    4) f��
STEP    32 / 35 (thread    3) f��
STEP    28 / 35 (thread    5) f��
STEP    33 / 35 (thread    0) f��
STEP    34 / 35 (thread    1) f��
Reallocating..done. *alloclen = 2146

STEP    35 / 35 (thread    2) f��
done.

Making a distance matrix from msa.. 

    0 / 36 (thread    0)
done.

Constructing a UPGMA tree (efffree=1) ... 

    0 / 36
   10 / 36
   20 / 36
   30 / 36
done.

Progressive alignment 2/2... 

STEP     1 / 35 (thread    0) f��
STEP     2 / 35 (thread    2)
STEP     3 / 35 (thread    5) f�� f��
STEP     4 / 35 (thread    1) f��
STEP     5 / 35 (thread    4) f��
STEP     8 / 35 (thread    0) f��
STEP     9 / 35 (thread    0) f��
STEP    10 / 35 (thread    2) f��
STEP     7 / 35 (thread    1) f��
STEP    11 / 35 (thread    5) f��
STEP    12 / 35 (thread    0) f��
STEP    14 / 35 (thread    5) f��
STEP     6 / 35 (thread    3) f��
STEP    16 / 35 (thread    5) f��
STEP    17 / 35 (thread    1) f��
STEP    18 / 35 (thread    5) f��
STEP    19 / 35 (thread    5) f��
STEP    20 / 35 (thread    5) f��
STEP    22 / 35 (thread    5) f��
STEP    13 / 35 (thread    2) f��
STEP    24 / 35 (thread    4) f��
STEP    15 / 35 (thread    0) f��
STEP    26 / 35 (thread    2) f��
STEP    25 / 35 (thread    4) f��
STEP    21 / 35 (thread    1) f��
STEP    29 / 35 (thread    2) f��
STEP    23 / 35 (thread    5) f��
STEP    27 / 35 (thread    0) f��
STEP    30 / 35 (thread    1) f��
STEP    28 / 35 (thread    3) f��
STEP    33 / 35 (thread    5) f��
STEP    31 / 35 (thread    4) f��
STEP    32 / 35 (thread    2) f��
STEP    34 / 35 (thread    0) f��
Reallocating..done. *alloclen = 2123

STEP    35 / 35 (thread    1) f��
done.

disttbfast (aa) Version 7.489
alg=A, model=BLOSUM62, 1.53, -0.00, -0.00, noshift, amax=0.0
6 thread(s)


Strategy:
 FFT-NS-2 (Fast but rough)
 Progressive method (guide trees were built 2 times.)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

Job Parameters:

Job parameter	Parameter value
datatype	`""`
cond_flavour	`{"__current_case__": 0, "flavourType": "mafft-fftns"}`
ep	`"0.0"`
op	`"1.53"`
matrix_condition	`{"BLOSUM": "62", "__current_case__": 1, "matrix": "BLOSUM"}`
reorder	`"false"`
getTree	`"false"`
outputFormat	`""`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"fasta"`

✅ toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft (Test test against test.galaxyproject.org #2)

Command Line:

Exit Code:

```
0
```

Standard Error:

nthread = 6
nthreadpair = 6
nthreadtb = 6
ppenalty_ex = 0
stacksize: -1 kb
rescale = 1
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 36 (thread    0)
done.

Constructing a UPGMA tree (efffree=0) ... 

    0 / 36
   10 / 36
   20 / 36
   30 / 36
done.

Progressive alignment 1/2... 

STEP     1 / 35 (thread    0) d��
STEP     2 / 35 (thread    3) d��
STEP     3 / 35 (thread    4) d��
STEP     4 / 35 (thread    1) d��
STEP     5 / 35 (thread    5) d��
STEP     8 / 35 (thread    3) d��
STEP     6 / 35 (thread    2) d��
STEP     9 / 35 (thread    3) d��
STEP    10 / 35 (thread    4) d��
STEP     7 / 35 (thread    1) d��
STEP    11 / 35 (thread    3) d��
STEP    12 / 35 (thread    4) d��
STEP    15 / 35 (thread    0) d��
STEP    16 / 35 (thread    5) d��
STEP    17 / 35 (thread    0) d��
STEP    18 / 35 (thread    2) d��
STEP    13 / 35 (thread    3) d��
STEP    20 / 35 (thread    1) d��
STEP    19 / 35 (thread    0) d��
STEP    21 / 35 (thread    2) d��
STEP    22 / 35 (thread    3) d��
STEP    14 / 35 (thread    4) d��
STEP    26 / 35 (thread    0) d��
STEP    23 / 35 (thread    5) d��
STEP    24 / 35 (thread    3) d��
STEP    30 / 35 (thread    3) d��
STEP    25 / 35 (thread    1) d��
STEP    32 / 35 (thread    0) d��
STEP    29 / 35 (thread    5) d��
STEP    27 / 35 (thread    2) d��
STEP    33 / 35 (thread    1) d��
STEP    28 / 35 (thread    4) d��
STEP    31 / 35 (thread    3) d��
STEP    34 / 35 (thread    0) d��
Reallocating..done. *alloclen = 2146

STEP    35 / 35 (thread    2) d�� h
done.

Making a distance matrix from msa.. 

    0 / 36 (thread    0)
done.

Constructing a UPGMA tree (efffree=1) ... 

    0 / 36
   10 / 36
   20 / 36
   30 / 36
done.

Progressive alignment 2/2... 

STEP     1 / 35 (thread    0) d��
STEP     2 / 35 (thread    3) d��
STEP     3 / 35 (thread    3) d��
STEP     4 / 35 (thread    0) d��
STEP     6 / 35 (thread    4) d��
STEP     7 / 35 (thread    0) d��
STEP     8 / 35 (thread    4) d��
STEP     9 / 35 (thread    0) d��
STEP    10 / 35 (thread    1) d��
STEP    11 / 35 (thread    4) d��
STEP    12 / 35 (thread    5) d��
STEP    14 / 35 (thread    2) d��
STEP     5 / 35 (thread    3) d��
STEP    16 / 35 (thread    0) d��
STEP    18 / 35 (thread    4) d��
STEP    19 / 35 (thread    0) d��
STEP    20 / 35 (thread    2) d��
STEP    21 / 35 (thread    0) d��
STEP    22 / 35 (thread    2) d��
STEP    13 / 35 (thread    1) d��
STEP    17 / 35 (thread    3) d��
STEP    15 / 35 (thread    5) d��
STEP    24 / 35 (thread    3) d��
STEP    25 / 35 (thread    5) d��
STEP    26 / 35 (thread    3) d��
STEP    23 / 35 (thread    2) d��
STEP    29 / 35 (thread    4) d��
STEP    28 / 35 (thread    5) d��
STEP    27 / 35 (thread    1) d��
STEP    31 / 35 (thread    0) d��
STEP    32 / 35 (thread    3) d��
STEP    30 / 35 (thread    2) d��
STEP    34 / 35 (thread    0) d��
STEP    33 / 35 (thread    1) d��
Reallocating..done. *alloclen = 2123

STEP    35 / 35 (thread    3) d�� h
done.

disttbfast (aa) Version 7.489
alg=A, model=BLOSUM62, 1.53, -0.00, -0.00, noshift, amax=0.0
6 thread(s)


Strategy:
 NW-NS-2 (Fast but rough)
 Progressive method (guide trees were built 2 times.)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

Job Parameters:

Job parameter	Parameter value
datatype	`""`
cond_flavour	`{"__current_case__": 3, "flavourType": "mafft-nwns"}`
ep	`"0.0"`
op	`"1.53"`
matrix_condition	`{"BLOSUM": "62", "__current_case__": 1, "matrix": "BLOSUM"}`
reorder	`"false"`
getTree	`"false"`
outputFormat	`"--clustalout"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"fasta"`

jennaj · 2022-03-08T22:38:09Z

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.489+galaxy0

mvdbeek · 2022-03-09T00:25:59Z

Results (powered by Planemo)

Summary

State	Count
Total	3
Passed	1
Error	0
Failure	2
Skipped	0

Failed s

❌ toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft (Test test against test.galaxyproject.org #2)

Problems:

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.489+galaxy0, exit_code: 255, stderr: FATAL:   container creation failed: mount /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft->/cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft error: while mounting /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft: while getting stat for /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft: stat /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft: input/output error

ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.489+galaxy0, exit_code: 255, stderr: FATAL:   container creation failed: mount /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft->/cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft error: while mounting /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft: while getting stat for /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft: stat /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft: input/output error

ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
.

Command Line:

Exit Code:

```
255
```

Standard Error:

FATAL:   container creation failed: mount /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft->/cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft error: while mounting /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft: while getting stat for /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft: stat /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft: input/output error

ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'

Job Parameters:

Job parameter	Parameter value
datatype	`""`
cond_flavour	`{"__current_case__": 3, "flavourType": "mafft-nwns"}`
ep	`"0.0"`
op	`"1.53"`
matrix_condition	`{"BLOSUM": "62", "__current_case__": 1, "matrix": "BLOSUM"}`
reorder	`"false"`
getTree	`"false"`
outputFormat	`"--clustalout"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"auto"`

❌ toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft (Test Test Prokka 1.14.6+galaxy1 #3)

Problems:

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.489+galaxy0, exit_code: 255, stderr: FATAL:   container creation failed: mount /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft->/cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft error: while mounting /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft: while getting stat for /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft: stat /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft: input/output error

ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.489+galaxy0, exit_code: 255, stderr: FATAL:   container creation failed: mount /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft->/cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft error: while mounting /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft: while getting stat for /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft: stat /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft: input/output error

ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
.

Command Line:

Exit Code:

```
255
```

Standard Error:

FATAL:   container creation failed: mount /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft->/cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft error: while mounting /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft: while getting stat for /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft: stat /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/mafft/f1a5908ea2cb/mafft: input/output error

ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'

Job Parameters:

Job parameter	Parameter value
datatype	`""`
cond_flavour	`{"__current_case__": 10, "dist_flavour": {"__current_case__": 4, "distance_method": "--fastapair", "weighti": "2.7"}, "fft": "true", "flavourType": "custom", "iterations": "1000", "score": "true"}`
ep	`"0.0"`
op	`"1.53"`
matrix_condition	`{"BLOSUM": "62", "__current_case__": 1, "matrix": "BLOSUM"}`
reorder	`"false"`
getTree	`"false"`
outputFormat	`"--clustalout"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"fasta"`

Passed s

✅ toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft (Test tool test #1)

Command Line:

Exit Code:

```
0
```

Standard Error:

nthread = 6
nthreadpair = 6
nthreadtb = 6
ppenalty_ex = 0
stacksize: -1 kb
rescale = 1
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 36 (thread    0)
done.

Constructing a UPGMA tree (efffree=0) ... 

    0 / 36
   10 / 36
   20 / 36
   30 / 36
done.

Progressive alignment 1/2... 

STEP     1 / 35 (thread    0)
STEP     3 / 35 (thread    5) f��
STEP     2 / 35 (thread    1) f��
STEP     4 / 35 (thread    3) f�� f��
STEP     8 / 35 (thread    5) f��
STEP     7 / 35 (thread    3) f��
STEP     5 / 35 (thread    2) f��
STEP     9 / 35 (thread    5) f��
STEP    10 / 35 (thread    0) f��
STEP    11 / 35 (thread    5) f��
STEP    12 / 35 (thread    1) f��
STEP     6 / 35 (thread    4) f��
STEP    15 / 35 (thread    1) f��
STEP    16 / 35 (thread    1) f��
STEP    17 / 35 (thread    3) f��
STEP    18 / 35 (thread    1) f��
STEP    20 / 35 (thread    2) f��
STEP    21 / 35 (thread    4) f��
STEP    13 / 35 (thread    0) f��
STEP    22 / 35 (thread    1) f��
STEP    19 / 35 (thread    3) f��
STEP    24 / 35 (thread    4) f��
STEP    26 / 35 (thread    0) f��
STEP    14 / 35 (thread    5) f��
STEP    23 / 35 (thread    3) f��
STEP    25 / 35 (thread    2) f��
STEP    29 / 35 (thread    4) f��
STEP    30 / 35 (thread    0) f��
STEP    27 / 35 (thread    1) f��
STEP    32 / 35 (thread    2) f��
STEP    28 / 35 (thread    5) f��
STEP    31 / 35 (thread    3) f��
STEP    33 / 35 (thread    0) f��
STEP    34 / 35 (thread    1) f��
Reallocating..done. *alloclen = 2146

STEP    35 / 35 (thread    4) f��
done.

Making a distance matrix from msa.. 

    0 / 36 (thread    0)
done.

Constructing a UPGMA tree (efffree=1) ... 

    0 / 36
   10 / 36
   20 / 36
   30 / 36
done.

Progressive alignment 2/2... 

STEP     1 / 35 (thread    0) f��
STEP     2 / 35 (thread    1) f��
STEP     3 / 35 (thread    2) f��
STEP     4 / 35 (thread    4) f��
STEP     6 / 35 (thread    5) f��
STEP     8 / 35 (thread    1) f��
STEP     7 / 35 (thread    2) f��
STEP     9 / 35 (thread    1) f��
STEP    10 / 35 (thread    1) f��
STEP    11 / 35 (thread    2) f��
STEP    12 / 35 (thread    1) f��
STEP     5 / 35 (thread    3) f��
STEP    14 / 35 (thread    0) f��
STEP    16 / 35 (thread    1) f��
STEP    18 / 35 (thread    1) f��
STEP    17 / 35 (thread    0) f��
STEP    19 / 35 (thread    1) f��
STEP    20 / 35 (thread    1) f��
STEP    22 / 35 (thread    1) f��
STEP    24 / 35 (thread    5) f��
STEP    21 / 35 (thread    0) f��
STEP    23 / 35 (thread    1) f��
STEP    26 / 35 (thread    5) f��
STEP    13 / 35 (thread    4) f��
STEP    15 / 35 (thread    2) f��
STEP    29 / 35 (thread    1) f��
STEP    28 / 35 (thread    4) f��
STEP    25 / 35 (thread    0) f��
STEP    30 / 35 (thread    5) f��
STEP    27 / 35 (thread    3) f��
STEP    31 / 35 (thread    2) f��
STEP    33 / 35 (thread    0) f��
STEP    32 / 35 (thread    1) f��
STEP    34 / 35 (thread    4) f��
Reallocating..done. *alloclen = 2123

STEP    35 / 35 (thread    5) f��
done.

disttbfast (aa) Version 7.489
alg=A, model=BLOSUM62, 1.53, -0.00, -0.00, noshift, amax=0.0
6 thread(s)


Strategy:
 FFT-NS-2 (Fast but rough)
 Progressive method (guide trees were built 2 times.)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

Job Parameters:

Job parameter	Parameter value
datatype	`""`
cond_flavour	`{"__current_case__": 0, "flavourType": "mafft-fftns"}`
ep	`"0.0"`
op	`"1.53"`
matrix_condition	`{"BLOSUM": "62", "__current_case__": 1, "matrix": "BLOSUM"}`
reorder	`"false"`
getTree	`"false"`
outputFormat	`""`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"auto"`

jennaj · 2022-03-10T18:31:25Z

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.489+galaxy0

mvdbeek · 2022-03-10T20:32:04Z

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/rnateam/mafft/rbc_mafft (Test tool test #1)

Problems:

```
[Errno Expecting value] : 0
```

Command Line:

Job Parameters:

Job parameter	Parameter value
datatype	`""`
cond_flavour	`{"__current_case__": 0, "flavourType": "mafft-fftns"}`
ep	`"0.0"`
op	`"1.53"`
matrix_condition	`{"BLOSUM": "62", "__current_case__": 1, "matrix": "BLOSUM"}`
reorder	`"false"`
getTree	`"false"`
outputFormat	`""`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"auto"`

❌ toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft (Test test against test.galaxyproject.org #2)

Problems:

```
[Errno Expecting value] : 0
```

Command Line:

Job Parameters:

Job parameter	Parameter value
outputFormat	`"--clustalout"`
datatype	`""`
cond_flavour	`{"__current_case__": 3, "flavourType": "mafft-nwns"}`
ep	`"0.0"`
op	`"1.53"`
matrix_condition	`{"BLOSUM": "62", "__current_case__": 1, "matrix": "BLOSUM"}`
reorder	`"false"`
getTree	`"false"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"fasta"`

❌ toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft (Test Test Prokka 1.14.6+galaxy1 #3)

Problems:

[Errno Expecting value] <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Frameset//EN" "http://www.w3.org/TR/html4/frameset.dtd">
<html>

<head>
<title>Galaxy</title>
<style type="text/css">
body
{
    font: 75% verdana, "Bitstream Vera Sans", geneva, arial, helvetica, helve, sans-serif;
    background: white url(//error/content_bg.png) top repeat-x;
    color: #303030;
    padding: 0;
    border: 0;
    margin: 0;
    margin-right: 0;
    margin-left: 0;
}

div.pageTitle
{
    font-size: x-large;
    font-weight: bold;
}

div.pageTitle a:link, div.pageTitle a:visited, div.pageTitle a:active, div.pageTitle a:hover
{
    text-decoration: none;
    color: #ece7f2;
}
/*a:link, a:visited, a:active
{
}*/
td.masthead
{
    vertical-align: middle;
    background: #023858 url(//error/masthead_bg.png) bottom;
    height: 40px;
    padding-left: 10px;
}
td.content
{
    vertical-align: top;
    padding: 10px;
}
a:link, a:visited, a:active
{
    color: #303030;
}
</style>
</head>
<table width="100%" border="0" cellspacing="0" cellpadding="0">
    <tr>
        <td class="masthead"><div class="pageTitle"><a target="_blank" href="http://galaxyproject.org">Galaxy</a></div></td>
    </tr>
    <tr>
        <td class="content">
            <h2>Galaxy could not be reached</h2>
            <p>
            
            
            You are seeing this message because a request to Galaxy timed out or was refused. This may be a temporary issue which
could be resolved by retrying the operation you were performing. If you receive this message repeatedly or for an
extended amount of time, please check for additional information on the
<a href="https://status.galaxyproject.org/">Galaxy status page</a> or the
<a href="https://twitter.com/galaxyproject">@galaxyproject Twitter feed</a>. If the issue is not addressed on those
sources, you may report it to the support team at
<a href='mailto:[email protected]'>[email protected]</a>
with details on what you were trying to do and the URL in the address bar.

                        
            </p>
        </td>
    </tr>
</table>

</html>
: 0

Output outputAlignment:  different than expected, difference (using diff):
( /tmp/tmp42eyuystmafft_custom_result.aln v. /tmp/tmp8deqz8rzmafft_custom_result.aln )
--- local_file
+++ history_data
@@ -1,233 +1,233 @@
-CLUSTAL format alignment by MAFFT F-INS-i (v7.455)
-
-
-1==             MN------------------------GTE--GDNFYVPFS--------NKTGL-ARSPYE
-2==             MN------------------------GTE--GPNFYVPFS--------NITGV-VRSPFE
-3==             MN------------------------GTE--GINFYVPMS--------NKTGV-VRSPFE
-4=p             MN------------------------GTE--GKNFYVPMS--------NRTGL-VRSPFE
-5=p             MN------------------------GTE--GNNFYVPLS--------NRTGL-VRSPFE
-6==             MK------------------------QVPEFHEDFYIPIP-------LDINNLSAYSPFL
-7==             MR------------------------KMS--EEEFYL------------FKNISSVGPWD
-8=opsin,        ------------------------------------------------------------
-9==             MAQQWSLQ-RLAGRHPQDS----YEDSTQ--SSIFTYTNS--------NS----TRGPFE
-10==            MAQQWSLQ-RLAGRHPQDS----YEDSTQ--SSIFTYTNS--------NS----TRGPFE
-11==            MTEAWNVAVFAARRSRDD------DDTTR--GSVFTYTNT--------NN----TRGPFE
-12==            MA-AWEAA-FAARRRHEE------EDTTR--DSVFTYTNS--------NN----TRGPFE
-13==            MS----------------------SNSSQ--------------AP--PNG----TPGPFD
-14==            MESG-NV-----------------------------------------SSSLFGNVSTAL
-15==            MEYH-NV------------------------------------------SSVLGNVSSVL
-16==            MEPLCNA------------------------------------------------SEPPL
-17==            MDALCNA------------------------------------------------SEPPL
-18==            MT-------------------------------------------------------NAT
-19==            MA-------------------------------------------------------NVT
********
*SNIP *
********
+13==            ------------------------------------------PAHPV
+14==            ------------------------------------------QTTAA
+15==            ------------------------------------------QTTAA
+16==            ------------------------------------------QTTAA
+17==            ------------------------------------------QTSAA
+18==            ---------------------------------------------KA
+19==            ---------------------------------------------KS
+20==            --------------------------------------------SKA
+21==            --------------------------------------------SKA
+22==            --------------------------------------------SKA
+23==            --------------------------------------------SKA
+24==            --------------------------------------------SKD
+25==            ------------------------------------------EKSNA
+26==            ------------------------------------------KIPEA
+27==            PPQGYPPQGYPPQGYPPQGYPPQGAPPQVEAPQGAPPQGVDNQAYQA
+28==            P-QGYPPQGYPPQGYPP---PPQGAPPQ-GAPPAAPPQGVDNQAYQA
+29==            ---------------------------------------CRKKGHDS
+30==            ---------------------------------------CGKKGHDT
+31=p            ---------------------------------------CGKKGHDT
+32==            -----------------------------------------------
+33=p            -----------------------------------------------
+34==            -----------------------------------------------
+35=p            -----------------------------------------------
+36==            ---------------------------------------VRRRRAPQ
+

Command Line:

Job Parameters:

Job parameter	Parameter value
datatype	`""`
cond_flavour	`{"__current_case__": 10, "dist_flavour": {"__current_case__": 4, "distance_method": "--fastapair", "weighti": "2.7"}, "fft": "true", "flavourType": "custom", "iterations": "1000", "score": "true"}`
ep	`"0.0"`
op	`"1.53"`
matrix_condition	`{"BLOSUM": "62", "__current_case__": 1, "matrix": "BLOSUM"}`
reorder	`"false"`
getTree	`"false"`
outputFormat	`"--clustalout"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"auto"`

jennaj · 2022-06-27T17:43:33Z

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.489+galaxy0

mvdbeek · 2022-06-27T23:07:36Z

Results (powered by Planemo)

Summary

State	Count
Total	3
Passed	0
Error	3
Failure	0
Skipped	0

Errored s

❌ toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft (Test tool test #1)
Execution Problem:
- Input staging problem: Expecting value: line 1 column 1 (char 0)
❌ toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft (Test test against test.galaxyproject.org #2)
Execution Problem:
- Input staging problem: Expecting value: line 1 column 1 (char 0)
❌ toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft (Test Test Prokka 1.14.6+galaxy1 #3)
Execution Problem:
- Input staging problem: Expecting value: line 1 column 1 (char 0)

jennaj mentioned this issue Feb 8, 2022

Update mafft to 7.489+galaxy0 galaxyproject/usegalaxy-playbook#351

Closed

mvdbeek mentioned this issue Feb 24, 2022

Test cutadapt 3.5+galaxy1 #22

Closed

mvdbeek mentioned this issue Nov 10, 2022

test cutadapt 4.0+galaxy1 #68

Closed

mvdbeek mentioned this issue May 11, 2023

test sklearn_searchcv/1.0.8.4 #92

Closed

jennaj closed this as completed Jun 12, 2023

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Test mafft 7.221.3 #12

Test mafft 7.221.3 #12

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Test mafft 7.221.3 #12

Test mafft 7.221.3 #12

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