hallamlab / mp_tutorial Goto Github PK

Okay maybe this is no surprise, but MLTreeMap fails because it is looking for mltreemap/mltreemap_calculation/data/tree_data/cog_list.txt. May not be an issue if we're going to try and drop a python version in there.

Niels

/Users/nielsh/mac/metapathways_python_mac/mltreemap/mltreemap_calculation/mltreemap.pl -i /Users/nielsh/mac/output/HOT_Sanger/1_upper_euphotic/preprocessed//1_upper_euphotic.fasta -o /Users/nielsh/mac/output/HOT_Sanger/1_upper_euphotic/mltreemap_calculations/ -e executables
Start MLTreeMap v2.061
ERROR: can't open /Users/nielsh/mac/metapathways_python_mac/mltreemap/mltreemap_calculation/data/tree_data/cog_list.txt!

could not open program on a MacBook Air Mac OS X 10.7.5

error message:

Process: MetaPathways2 [1511]
Path: /Volumes/VOLUME/MetaPathways2.app/Contents/MacOS/MetaPathways2
Identifier: com.yourcompany.MetaPathways2
Version: ??? (???)
Code Type: X86-64 (Native)
Parent Process: launchd [121]

Date/Time: 2014-03-16 15:21:28.386 -0700
OS Version: Mac OS X 10.7.5 (11G63b)
Report Version: 9

Interval Since Last Report: 555746 sec
Crashes Since Last Report: 6
Per-App Interval Since Last Report: 116 sec
Per-App Crashes Since Last Report: 6
Anonymous UUID: 6FABFC52-5A33-4E76-B592-1F5EB6817FD7

Crashed Thread: 0 Dispatch queue: com.apple.main-thread

Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_PROTECTION_FAILURE at 0x00007fff5f3fff88

VM Regions Near 0x7fff5f3fff88:
CG shared images 00000001c5c92000-00000001c5c9a000 [ 32K] r--/r-- SM=SHM
--> STACK GUARD 00007fff5bc00000-00007fff5f400000 [ 56.0M] ---/rwx SM=NUL stack guard for thread 0
Stack 00007fff5f400000-00007fff5fc00000 [ 8192K] rw-/rwx SM=COW thread 0

Application Specific Information:
objc[1511]: garbage collection is OFF

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libsystem_c.dylib 0x00007fff8b1560c6 __getcwd + 51
1 libsystem_c.dylib 0x00007fff8b156347 __private_getcwd + 209
2 QtCore 0x0000000100e1ce72 0x100c6c000 + 1773170
3 QtCore 0x0000000100db73aa QDir::currentPath() + 26
4 com.yourcompany.MetaPathways2 0x0000000100039340 RunData::setupDefaultConfig() + 160
5 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
6 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
7 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
8 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
9 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
10 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
11 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
12 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
13 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
14 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
15 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
16 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
17 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
18 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
19 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
20 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
21 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
22 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
23 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
24 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
25 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
26 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
27 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
28 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
29 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
30 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
31 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
32 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
33 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
34 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
35 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
36 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
37 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
38 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
39 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
40 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
41 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
42 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
43 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
44 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
45 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
46 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
47 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
48 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
49 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
50 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
51 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
52 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
53 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
54 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
55 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
56 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
57 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
58 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
59 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
60 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
61 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
62 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
63 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
64 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
65 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
66 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
67 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
68 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
69 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
70 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
71 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
72 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
73 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
74 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
75 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
76 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
77 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
78 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
79 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
80 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
81 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
82 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
83 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
84 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
85 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
86 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
87 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
88 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
89 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
90 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
91 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
92 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
93 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
94 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
95 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
96 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
97 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
98 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
99 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
100 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
101 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
102 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
103 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
104 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
105 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
106 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
107 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
108 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
109 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
110 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
111 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
112 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
113 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
114 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
115 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
116 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
117 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
118 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
119 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
120 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
121 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
122 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
123 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
124 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
125 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
126 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
127 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
128 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
129 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
130 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
131 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
132 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
133 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
134 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
135 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
136 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
137 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
138 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
139 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
140 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
141 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
142 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
143 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
144 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
145 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
146 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
147 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
148 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
149 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
150 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
151 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
152 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
153 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
154 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
155 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
156 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
157 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
158 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
159 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
160 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
161 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
162 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
163 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
164 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
165 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
166 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
167 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
168 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
169 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
170 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
171 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
172 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
173 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
174 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
175 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
176 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
177 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
178 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
179 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
180 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
181 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
182 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
183 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
184 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
185 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
186 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
187 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
188 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
189 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
190 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
191 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
192 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
193 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
194 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
195 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
196 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
197 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
198 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
199 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
200 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
201 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
202 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
203 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
204 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
205 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
206 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
207 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
208 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
209 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
210 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
211 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
212 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
213 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
214 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
215 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
216 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
217 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
218 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
219 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
220 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
221 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
222 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
223 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
224 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
225 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
226 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
227 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
228 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
229 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
230 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
231 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
232 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
233 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
234 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
235 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
236 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
237 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
238 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
239 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
240 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
241 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
242 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
243 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
244 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
245 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
246 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
247 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
248 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
249 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
250 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
251 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
252 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
253 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
254 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
255 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
256 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
257 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
258 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
259 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
260 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
261 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
262 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
263 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
264 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
265 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
266 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
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272 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
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348 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
349 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
350 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
351 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
352 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
353 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
354 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
355 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
356 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
357 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
358 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
359 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
360 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
361 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
362 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
363 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
364 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
365 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
366 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
367 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
368 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
369 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
370 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
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372 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
373 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
374 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
375 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
376 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
377 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
378 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
379 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
380 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
381 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
382 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
383 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
384 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
385 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
386 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
387 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
388 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
389 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
390 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
391 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
392 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
393 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
394 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
395 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
396 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
397 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
398 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
399 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
400 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
401 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
402 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
403 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
404 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
405 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
406 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
407 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
408 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
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435 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
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440 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
441 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
442 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
443 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
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458 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
459 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
460 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
461 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
462 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
463 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
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502 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
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508 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
509 com.yourcompany.MetaPathways2 0x000000010003a047 RunData::setupDefaultConfig() + 3495
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Thread 1:: Dispatch queue: com.apple.libdispatch-manager
0 libsystem_kernel.dylib 0x00007fff928ec7e6 kevent + 10
1 libdispatch.dylib 0x00007fff8a3bf786 _dispatch_mgr_invoke + 923
2 libdispatch.dylib 0x00007fff8a3be316 _dispatch_mgr_thread + 54

Thread 2:
0 libsystem_kernel.dylib 0x00007fff928ec192 __workq_kernreturn + 10
1 libsystem_c.dylib 0x00007fff8b16d594 _pthread_wqthread + 758
2 libsystem_c.dylib 0x00007fff8b16eb85 start_wqthread + 13

Thread 3:
0 libsystem_kernel.dylib 0x00007fff928ec192 __workq_kernreturn + 10
1 libsystem_c.dylib 0x00007fff8b16d594 _pthread_wqthread + 758
2 libsystem_c.dylib 0x00007fff8b16eb85 start_wqthread + 13

Thread 4:

Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x08fb8d87bc6dc000 rbx: 0x0000000000000400 rcx: 0x00007fff928ece9e rdx: 0x0000000000000001
rdi: 0x00007fff8b1c5a08 rsi: 0x0000000000000000 rbp: 0x00007fff5f4000e0 rsp: 0x00007fff5f3fff90
r8: 0x0000000000000002 r9: 0x0000000000000000 r10: 0x0000000000013dc0 r11: 0x0000000000000202
r12: 0x0000000101d69138 r13: 0x0000000106b41ef8 r14: 0x00007fff5f4002d0 r15: 0x00007fff5f400710
rip: 0x00007fff8b1560c6 rfl: 0x0000000000010246 cr2: 0x00007fff5f3fff88
Logical CPU: 0

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0x7fff958f0000 - 0x7fff95918fff com.apple.PerformanceAnalysis (1.11 - 11) <8D4C6382-DD92-37A2-BCFC-E89951320848> /System/Library/PrivateFrameworks/PerformanceAnalysis.framework/Versions/A/PerformanceAnalysis
0x7fff95d93000 - 0x7fff95da9ff7 com.apple.ImageCapture (7.1.0 - 7.1.0) <1AD40E02-2126-377B-A0D2-CBB21D932558> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ImageCapture.framework/Versions/A/ImageCapture
0x7fff95daa000 - 0x7fff961d7fff libLAPACK.dylib (??? - ???) <4F2E1055-2207-340B-BB45-E4F16171EE0D> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
0x7fff961d8000 - 0x7fff963dafff libicucore.A.dylib (46.1.0 - compatibility 1.0.0) <0176782F-9526-3905-813A-7A5676EC2C86> /usr/lib/libicucore.A.dylib
0x7fff963db000 - 0x7fff9657bff7 com.apple.QuartzCore (1.7 - 270.5) <19E5E0AB-DAA9-3F97-988C-D9A46AFB9C04> /System/Library/Frameworks/QuartzCore.framework/Versions/A/QuartzCore
0x7fff9657c000 - 0x7fff965d7ff7 com.apple.opencl (2.0.19 - 2.0.19) /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL
0x7fff965de000 - 0x7fff965f5fff com.apple.MultitouchSupport.framework (231.4 - 231.4) <10A978D1-8781-33F0-BE45-60C9171F7278> /System/Library/PrivateFrameworks/MultitouchSupport.framework/Versions/A/MultitouchSupport
0x7fff965f8000 - 0x7fff96660ff7 com.apple.coreui (1.2.2 - 165.11) <9316266A-39CA-3EC7-9C9E-726462CEFF4D> /System/Library/PrivateFrameworks/CoreUI.framework/Versions/A/CoreUI
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0x7fff9679d000 - 0x7fff96881ff7 com.apple.CoreServices.OSServices (478.50 - 478.50) <3D6AA4EF-C601-36C7-8F3A-A00964F01759> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices
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0x7fff968e7000 - 0x7fff968f5fff com.apple.NetAuth (3.1 - 3.1) /System/Library/PrivateFrameworks/NetAuth.framework/Versions/A/NetAuth
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External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 4
thread_create: 0
thread_set_state: 0
Calls made by this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by all processes on this machine:
task_for_pid: 5442
thread_create: 1
thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=172.4M resident=80.6M(47%) swapped_out_or_unallocated=91.7M(53%)
Writable regions: Total=132.4M written=50.4M(38%) resident=79.1M(60%) swapped_out=0K(0%) unallocated=53.3M(40%)

REGION TYPE VIRTUAL
=========== =======
ATS (font support) 31.9M
ATS (font support) (reserved) 4K reserved VM address space (unallocated)
CG shared images 1224K
CoreGraphics 16K
CoreServices 2488K
MALLOC 71.9M
MALLOC guard page 48K
STACK GUARD 56.0M
Stack 9756K
Stack (reserved) 520K reserved VM address space (unallocated)
VM_ALLOCATE 16.1M
__CI_BITMAP 80K
__DATA 13.0M
__IMAGE 528K
__LINKEDIT 52.7M
__TEXT 119.6M
__UNICODE 544K
mapped file 71.0M
shared memory 312K
=========== =======
TOTAL 447.4M
TOTAL, minus reserved VM space 446.9M

Model: MacBookAir3,1, BootROM MBA31.0061.B07, 2 processors, Intel Core 2 Duo, 1.4 GHz, 4 GB, SMC 1.67f10
Graphics: NVIDIA GeForce 320M, NVIDIA GeForce 320M, PCI, 256 MB
Memory Module: BANK 0/DIMM0, 2 GB, DDR3, 1067 MHz, 0x80AD, 0x484D54333235533642465238412D47372020
Memory Module: BANK 1/DIMM0, 2 GB, DDR3, 1067 MHz, 0x80AD, 0x484D54333235533642465238412D47372020
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0xD1), Broadcom BCM43xx 1.0 (5.106.198.19.22)
Bluetooth: Version 4.0.8f17, 2 service, 18 devices, 1 incoming serial ports
Network Service: AirPort, AirPort, en0
Serial ATA Device: APPLE SSD TS064C, 60.67 GB
USB Device: FaceTime Camera (Built-in), apple_vendor_id, 0x850a, 0x24600000 / 2
USB Device: BRCM2070 Hub, 0x0a5c (Broadcom Corp.), 0x4500, 0x04500000 / 3
USB Device: Bluetooth USB Host Controller, apple_vendor_id, 0x821b, 0x04530000 / 5
USB Device: Apple Internal Keyboard / Trackpad, apple_vendor_id, 0x0242, 0x04300000 / 2

All the defaults are correct except for the Minimum BSR which is 0.0. This is different than the usual default of 0.4 Is there a reason for this?

The comparison table sorts its entries when you click on the header tab, however, it also needs to resize the column based on the longest entry so that it can be read.

With the binary that was released in win_v2, users may experience behavior where the program seems to launch, and then immediately crashes.

tRNAscan1.4 can't find some file TPCsignal.

['LSURef_115_tax_silva_2013-12-12']
WARNING: Refseq annotation is not scheduled!
         Taxonomic information will not be found in the annotation table.
{'bitscore': '50', 'similarity': '20', 'evalue': '0.000001', 'length': 180, 'output': '/Users/nielsh/mac/output/HOT_Sanger/1_upper_euphotic/results//rRNA/1_upper_euphotic.lsuref_115_tax_silva_2013-12-12.rRNA.stats.txt', 'blast_files': ['/Users/nielsh/mac/output/HOT_Sanger/1_upper_euphotic/blast_results//1_upper_euphotic.rRNA.lsuref_115_tax_silva_2013-12-12.blastout'], 'fasta': None, 'tax_databases': ['/Users/nielsh/mac/metapathways_python_mac/blastDB//taxonomic/LSURef_115_tax_silva_2013-12-12']}
{'length': 180, 'bitscore': 50.0, 'evalue': 9.9999999999999995e-07, 'similarity': 20.0}
Error! : tRNAscan1.4: main cannot open TPCsignal consensus file
ERROR: Path for "TBL2ASN_EXECUTABLE" is NOT set properly in configuration file "/Users/nielsh/mac/metapathways_python_mac/template_config.txt"
ERROR: Currently it is set to "/Users/nielsh/mac/metapathways_python_mac/executables/mac/bit64/tbl2asn"

['LSURef_115_tax_silva_2013-12-12']
WARNING: Refseq annotation is not scheduled!
         Taxonomic information will not be found in the annotation table.
{'bitscore': '50', 'similarity': '20', 'evalue': '0.000001', 'length': 180, 'output': '/Users/nielsh/mac/output/HOT_Sanger/2_chlorophyllmax/results//rRNA/2_chlorophyllmax.lsuref_115_tax_silva_2013-12-12.rRNA.stats.txt', 'blast_files': ['/Users/nielsh/mac/output/HOT_Sanger/2_chlorophyllmax/blast_results//2_chlorophyllmax.rRNA.lsuref_115_tax_silva_2013-12-12.blastout'], 'fasta': None, 'tax_databases': ['/Users/nielsh/mac/metapathways_python_mac/blastDB//taxonomic/LSURef_115_tax_silva_2013-12-12']}
{'length': 180, 'bitscore': 50.0, 'evalue': 9.9999999999999995e-07, 'similarity': 20.0}
Error! : tRNAscan1.4: main cannot open TPCsignal consensus file
ERROR: Path for "TBL2ASN_EXECUTABLE" is NOT set properly in configuration file "/Users/nielsh/mac/metapathways_python_mac/template_config.txt"
ERROR: Currently it is set to "/Users/nielsh/mac/metapathways_python_mac/executables/mac/bit64/tbl2asn"

['LSURef_115_tax_silva_2013-12-12']
WARNING: Refseq annotation is not scheduled!
         Taxonomic information will not be found in the annotation table.
{'bitscore': '50', 'similarity': '20', 'evalue': '0.000001', 'length': 180, 'output': '/Users/nielsh/mac/output/HOT_Sanger/3_below_euphotic/results//rRNA/3_below_euphotic.lsuref_115_tax_silva_2013-12-12.rRNA.stats.txt', 'blast_files': ['/Users/nielsh/mac/output/HOT_Sanger/3_below_euphotic/blast_results//3_below_euphotic.rRNA.lsuref_115_tax_silva_2013-12-12.blastout'], 'fasta': None, 'tax_databases': ['/Users/nielsh/mac/metapathways_python_mac/blastDB//taxonomic/LSURef_115_tax_silva_2013-12-12']}
{'length': 180, 'bitscore': 50.0, 'evalue': 9.9999999999999995e-07, 'similarity': 20.0}
Error! : tRNAscan1.4: main cannot open TPCsignal consensus file
ERROR: Path for "TBL2ASN_EXECUTABLE" is NOT set properly in configuration file "/Users/nielsh/mac/metapathways_python_mac/template_config.txt"
ERROR: Currently it is set to "/Users/nielsh/mac/metapathways_python_mac/executables/mac/bit64/tbl2asn"

['LSURef_115_tax_silva_2013-12-12']
WARNING: Refseq annotation is not scheduled!
         Taxonomic information will not be found in the annotation table.
{'bitscore': '50', 'similarity': '20', 'evalue': '0.000001', 'length': 180, 'output': '/Users/nielsh/mac/output/HOT_Sanger/4_deepabyss/results//rRNA/4_deepabyss.lsuref_115_tax_silva_2013-12-12.rRNA.stats.txt', 'blast_files': ['/Users/nielsh/mac/output/HOT_Sanger/4_deepabyss/blast_results//4_deepabyss.rRNA.lsuref_115_tax_silva_2013-12-12.blastout'], 'fasta': None, 'tax_databases': ['/Users/nielsh/mac/metapathways_python_mac/blastDB//taxonomic/LSURef_115_tax_silva_2013-12-12']}
{'length': 180, 'bitscore': 50.0, 'evalue': 9.9999999999999995e-07, 'similarity': 20.0}
Error! : tRNAscan1.4: main cannot open TPCsignal consensus file
ERROR: Path for "TBL2ASN_EXECUTABLE" is NOT set properly in configuration file "/Users/nielsh/mac/metapathways_python_mac/template_config.txt"
ERROR: Currently it is set to "/Users/nielsh/mac/metapathways_python_mac/executables/mac/bit64/tbl2asn"

['LSURef_115_tax_silva_2013-12-12']
WARNING: Refseq annotation is not scheduled!
         Taxonomic information will not be found in the annotation table.
{'bitscore': '50', 'similarity': '20', 'evalue': '0.000001', 'length': 180, 'output': '/Users/nielsh/mac/output/HOT_Sanger/5_uppermesopelagic/results//rRNA/5_uppermesopelagic.lsuref_115_tax_silva_2013-12-12.rRNA.stats.txt', 'blast_files': ['/Users/nielsh/mac/output/HOT_Sanger/5_uppermesopelagic/blast_results//5_uppermesopelagic.rRNA.lsuref_115_tax_silva_2013-12-12.blastout'], 'fasta': None, 'tax_databases': ['/Users/nielsh/mac/metapathways_python_mac/blastDB//taxonomic/LSURef_115_tax_silva_2013-12-12']}
{'length': 180, 'bitscore': 50.0, 'evalue': 9.9999999999999995e-07, 'similarity': 20.0}
Error! : tRNAscan1.4: main cannot open TPCsignal consensus file
ERROR: Path for "TBL2ASN_EXECUTABLE" is NOT set properly in configuration file "/Users/nielsh/mac/metapathways_python_mac/template_config.txt"
ERROR: Currently it is set to "/Users/nielsh/mac/metapathways_python_mac/executables/mac/bit64/tbl2asn"

['LSURef_115_tax_silva_2013-12-12']
WARNING: Refseq annotation is not scheduled!
         Taxonomic information will not be found in the annotation table.
{'bitscore': '50', 'similarity': '20', 'evalue': '0.000001', 'length': 180, 'output': '/Users/nielsh/mac/output/HOT_Sanger/6_upper_euphotic/results//rRNA/6_upper_euphotic.lsuref_115_tax_silva_2013-12-12.rRNA.stats.txt', 'blast_files': ['/Users/nielsh/mac/output/HOT_Sanger/6_upper_euphotic/blast_results//6_upper_euphotic.rRNA.lsuref_115_tax_silva_2013-12-12.blastout'], 'fasta': None, 'tax_databases': ['/Users/nielsh/mac/metapathways_python_mac/blastDB//taxonomic/LSURef_115_tax_silva_2013-12-12']}
{'length': 180, 'bitscore': 50.0, 'evalue': 9.9999999999999995e-07, 'similarity': 20.0}
Error! : tRNAscan1.4: main cannot open TPCsignal consensus file
ERROR: Path for "TBL2ASN_EXECUTABLE" is NOT set properly in configuration file "/Users/nielsh/mac/metapathways_python_mac/template_config.txt"
ERROR: Currently it is set to "/Users/nielsh/mac/metapathways_python_mac/executables/mac/bit64/tbl2asn"

['LSURef_115_tax_silva_2013-12-12']
WARNING: Refseq annotation is not scheduled!
         Taxonomic information will not be found in the annotation table.
{'bitscore': '50', 'similarity': '20', 'evalue': '0.000001', 'length': 180, 'output': '/Users/nielsh/mac/output/HOT_Sanger/7_omz/results//rRNA/7_omz.lsuref_115_tax_silva_2013-12-12.rRNA.stats.txt', 'blast_files': ['/Users/nielsh/mac/output/HOT_Sanger/7_omz/blast_results//7_omz.rRNA.lsuref_115_tax_silva_2013-12-12.blastout'], 'fasta': None, 'tax_databases': ['/Users/nielsh/mac/metapathways_python_mac/blastDB//taxonomic/LSURef_115_tax_silva_2013-12-12']}
{'length': 180, 'bitscore': 50.0, 'evalue': 9.9999999999999995e-07, 'similarity': 20.0}
Error! : tRNAscan1.4: main cannot open TPCsignal consensus file

We have kind of fought hard for some these settings to be the same:

ORF Annotation Parameters:
Minimum BSR 0.4
Maximum Hits: 5
Minimum Score: 20
Minimum Length: 60
Minimum Evalue: 0.000001

rRNA Annotation Parameters
Minimum Identity: 20%
Minimum Bitscore: 50
Maximum EValue: 0.000001

I am running Mac OS X 10.8.4 and MetaPathways 2.0. I've been trying to look at the data that we are currently examining in our class but I noticed that MetaPathways 2.0 seems to crash at some points. More specifically, I've noticed that it crashes either in the absence of data or when you don't change the file input format.
ie: If you choose an input folder and output folder under "Stages" that uses .fasta and leave it as gbk-annotated --> go to "Results" and check "comparative mode" --> Select samples (which appears blank) --> hit OK --> MetaPathways 2.0 crashes
Alternatively, if you don't load any input or output folder and go to "Results" and check comparative mode --> select samples --> hit OK --> MetaPathways 2.0 crashes.

Sarpreet Sekhon
MICB 425

When you export a file there is some strange behavior for adding .txt to everything. It should only due this in the case there is not already a .txt in the user's filename.

• compared multiple samples
• exported COG all options
• tried to export METACYC all options
• program hangs

MetaPathways 2.0, Mac OS 10.6.8.
GUI does not respond to mouse or keyboard after "Hiding" and "Unhiding" app. Need to restart app to use again.

After a run, when you click on the results tab, results are not automatically loaded so the combo-box is empty. The are not loaded until you click the 'Load Results' button, then the combo-box will load with your samples.

This is is somewhat unintuitive, the tab switch should be good enough.

Hi,
I am trying to run MetaPathways in OS X version 10.9.5, but I haven't be able to use it. I'm running in command line usig:

/Users/ejb/MetaPathways2/MetaPathways.py -i /Users/ejb/Desktop/prueba/WGS-Mock-community_GES14_03577_AGCGATAGGTACTGAC_DD_RF_CLEAN_TRIM_MASK.fasta -o /Users/ejb/Desktop/prueba/prueba_output -c /Users/ejb/MetaPathways2/config/template_config.txt -p /Users/ejb/MetaPathways2/config/template_param.txt -r overwrite -v

But it is not doing anything only print it out this info in the terminal window:

from: can't read /var/mail/future
/Users/ejb/MetaPathways2/MetaPathways.py: line 3: author: command not found
/Users/ejb/MetaPathways2/MetaPathways.py: line 4: copyright: command not found
/Users/ejb/MetaPathways2/MetaPathways.py: line 5: credits: command not found
/Users/ejb/MetaPathways2/MetaPathways.py: line 6: version: command not found
/Users/ejb/MetaPathways2/MetaPathways.py: line 7: maintainer: command not found
/Users/ejb/MetaPathways2/MetaPathways.py: line 8: status: command not found
/Users/ejb/MetaPathways2/MetaPathways.py: line 13: try:: command not found
/Users/ejb/MetaPathways2/MetaPathways.py: line 14: import: command not found
from: can't read /var/mail/os
from: can't read /var/mail/optparse
from: can't read /var/mail/libs.python_modules.utils
from: can't read /var/mail/libs.python_modules.utils.utils
from: can't read /var/mail/libs.python_modules.utils.metapathways_utils
from: can't read /var/mail/libs.python_modules.parsers.parse
from: can't read /var/mail/libs.python_modules.pipeline.metapathways_pipeline
from: can't read /var/mail/libs.python_modules.utils.sysutil
from: can't read /var/mail/libs.python_modules.pipeline.metapathways
from: can't read /var/mail/libs.python_modules.annotate
from: can't read /var/mail/libs.python_modules.grid.blast_using_grid
from: can't read /var/mail/libs.python_modules.diagnostics.parameters
from: can't read /var/mail/libs.python_modules.diagnostics.diagnoze
from: can't read /var/mail/libs.python_modules.pipeline.sampledata
/Users/ejb/MetaPathways2/MetaPathways.py: line 32: except:: command not found
/Users/ejb/MetaPathways2/MetaPathways.py: line 33: print: command not found
/Users/ejb/MetaPathways2/MetaPathways.py: line 34: print: command not found
/Users/ejb/MetaPathways2/MetaPathways.py: line 35: print: command not found
/Users/ejb/MetaPathways2/MetaPathways.py: line 37: syntax error near unexpected token 3' /Users/ejb/MetaPathways2/MetaPathways.py: line 37: sys.exit(3)'

Thanks for your help.
Regards,
Eddy

The linux build requires libraries to be dynamically loaded. This should hopefully be resolved soon.

In the results tab, when search ("filtering") is on, let the user know. For example, show the current search string at the window bottom, otherwise there's no way of telling what is shown or not. Even re-opening the search menu does not give any clue: the search box defaults to empty again.

Thanks!

setDefaultConfig() will fail repeatedly if there are spaces in the paths of values. For example, if any of the python, perl, mp path, pathway tools paths have spaces in user provided input, the program cannot update the file and will crash silently.

The only way to search the functional and taxonomic table is by Column: ALL

Other tables allow you to select a specific column

• Loaded samples
• Pressed export
• Unable to exit export window using the cancel button. Clicking the button does nothing.

Able to exit the window by clicking the window's "X", or by exporting as normal.

OS: Windows 8.1 Pro
Version: Metapathways v2.0 Windows

ERROR: Path for "TBL2ASN_EXECUTABLE" is NOT set properly in configuration file "/Users/nielsh/mac/metapathways_python_mac/template_config.txt"
ERROR: Currently it is set to "/Users/nielsh/mac/metapathways_python_mac/executables/mac/bit64/tbl2asn"

When navigating a hierarchy, the hide zero rows option is not respected when moving up or down levels.

Hide zero rows only seems to have consistent behaviour when showing "Show hierarchy " is clicked. In fact, the ORF Count column can be empty.

MetaPathways 2.0. Mac OS 10.6.8.

Call to prodigal fails. When running ORF prediction (by calling prodigal) in MetaPathways, the following error is generated:

/Applications/MetaPathways/executables/mac/bit64/prodigal  -m -p meta -f gff -i /Users/SteliosLouca/Desktop/UNI/Summer schools and Workshops/MetaPathways workshop/HOT test/7_omz/preprocessed//7_omz.fasta -o /Users/SteliosLouca/Desktop/UNI/Summer schools and Workshops/MetaPathways workshop/HOT test/7_omz/orf_prediction/7_omz.gff 
Error!:
Unknown option.

The correct prodigal command should rather be:

/Applications/MetaPathways/executables/mac/bit64/prodigal  -m -p meta -f gff -i "/Users/SteliosLouca/Desktop/UNI/Summer schools and Workshops/MetaPathways workshop/HOT_Sanger/7_omz/preprocessed//7_omz.fasta" -o "/Users/SteliosLouca/Desktop/UNI/Summer schools and Workshops/MetaPathways workshop/HOT test/7_omz/orf_prediction/7_omz.gff"

This works for me when run directly from the terminal. The necessary corrections are described below:

1. Put paths into quotes " ". This is necessary on Mac when paths have spaces or special characters (I guess escaping spaces would also do).
2. The input file path passed to prodigal was a weird hybrid between the should-be input & output path.

The metapathways app seems to use a lot of memory which makes the application really slow. I left it running over the weekend, so maybe there still a memory leak somewhere.

Predicted pathway tables need to changed a bit for R-compatibility:

• there's still funny characters on the that mess up the parsing ;'"&<space>
• exported tables need headers
• because the MetaCyc hierarchy is unbalanced there is a mixture of pathways and reactions currently being plotted, this should be modified so only MetaCyc base pathways are shown

The command that I'd like to target in R for import is

data <- read.table("filename.tsv.txt", sep="\t", header=T, rownames=1)

Seems you can't just add any nucleotide sequence to the taxonomic database list. I suspect if not an accepted name the rRNA stats step will hang.

Added just a few files containing a 16S genes but hags at the rRNA step:

Just a note that after installing Perl, Python and Pathway Tools, ARB no longer works. I'm not sure what interference is going on there but thought I would mention it.

Cheers,
Sheryl

When doing a comparative analysis one of things that everyone uses is a table of the raw counts of each step:

This might be something we add to the python code that the GUI can pick up.

Changing the file path or file name of the MetaPathways Directory after the Setup won't allow the program to launch.

1. Initial setup of loading the five files (executables and directories)
2. Exited the program
3. Moved/Renamed the MetaPathways Directory folder that was used in the Setup
4. Tried to open the program and crashed.

Restoring to the original file path or file name of the MetaPathways Directory that was entered in the current (or previous) Setup, the program can be launched.

OS: Mac OS X 10.9.2 and Windows 8
Version: MetaPathways2.0

GUI does not seem to launch in linux. Executable may not be built correctly?

Sometimes when jumping back and forth between the stages and parameters tabs the File Input Format changes to gbk-annotated. Haven't been able to systematically reproduce the bug.

I am using Mac OS X version 10.6.8 and was able to open Metapathway 1.0, but am unable to open Metapathways 2.0. Specifically, the application loads after ~1-3 minutes and an application image/icon appears, shortly after which I am given the message "application quit unexpectedly." I have been working at this for some time now, and have attempted to re-download the application, but to no avail.

Sunjit Parmar
44944106

This text should be changed in the setup to Pathway Tools Executable. This was confusing for people because there is no such thing as the PathoLogic executable only pathway-tools

• Selected sample
• Increased level to 1 (or 2)
• Exported
• Selected all columns
• Included contigs in export format
• MP2 crashes
  

Crash occurs at level 1 and level 2, but not level 0. Also occurs in comparative mode.

OS: Windows 8.1 Pro
Version: Metapathways v2.0 Windows

Mac OS 10.8.5
MP 2.1.3
Loading HOT (Sanger) data set results works. But when I click on the ORF column (in KEGG, COG etc) the column is selected but no sorting takes place.

People are red-green color blind. Red and blue or blue and orange might be better choices.

It would be better for this to pop in-front of the current window as it can get lost behind other windows if they there are a number of other softwares running.

When you click on a table header it sorts it as well as resizes it so that you can read everything. These should be separate actions. For simplicity this might be a 'right-click' option.

In the FUNC TAX table the exporter does not seem to respect your input, always outputting the whole table. Although it does seem to respect your separator tabs or commas:

shebop:Desktop nielsh$ head megan_test_tsv.txt
ORF_ID  ORF_length  start   end Contig_Name Contig_length   strand  ec  taxonomy    product
2_chlorophyllmax_1058_0 584 1   585 2_chlorophyllmax_1058   646 +   6.1.1.15    beta subdivision methylotrophs  synthetase OS Uncultured termite group 1 bacterium phylotype Rs-D17 GN proS PE 3 SV
2_chlorophyllmax_1058_1 77  569 646 2_chlorophyllmax_1058   646 +   -   -   hypothetical protein
2_chlorophyllmax_5798_0 725 94  819 2_chlorophyllmax_5798   971 +   -   -   hypothetical protein
2_chlorophyllmax_5799_0 860 96  956 2_chlorophyllmax_5799   958 -   -   -   hypothetical protein

or CSV

shebop:Desktop nielsh$ head test_megan.csv
ORF_ID,ORF_length,start,end,Contig_Name,Contig_length,strand,ec,taxonomy,product
2_chlorophyllmax_1058_0,584,1,585,2_chlorophyllmax_1058,646,+,6.1.1.15,beta subdivision methylotrophs,synthetase OS Uncultured termite group 1 bacterium phylotype Rs-D17 GN proS PE 3 SV
2_chlorophyllmax_1058_1,77,569,646,2_chlorophyllmax_1058,646,+,-,-,hypothetical protein
2_chlorophyllmax_5798_0,725,94,819,2_chlorophyllmax_5798,971,+,-,-,hypothetical protein
2_chlorophyllmax_5799_0,860,96,956,2_chlorophyllmax_5799,958,-,-,-,hypothetical protein
2_chlorophyllmax_5028_0,230,34,264,2_chlorophyllmax_5028,840,+,-,Actinobacteria Stackebrandt et al. 1997,preprotein translocase subunit SecG

But in both cases I only wanted certain columns selected:

It also didn't seem to output the sequence files ether.

In comparative mode, the output respected commas or tabs, but the directory mp_test_output.csv.txt.txt/ was also created. This directory should only be output if sequences are requested.

These red messages are also pretty awkward, we should use a window like everyone else...

As a little touch, the c++ app should have an icon.

Going straight to comparative mode without loading a sample (hash) then the program will fail.

Process:         MetaPathways2 [71842]
Path:            /Applications/MetaPathways2.app/Contents/MacOS/MetaPathways2
Identifier:      com.yourcompany.MetaPathways2
Version:         ??? (???)
Code Type:       X86-64 (Native)
Parent Process:  launchd [15747]

Date/Time:       2014-03-12 17:53:21.020 -0700
OS Version:      Mac OS X 10.6.8 (10K549)
Report Version:  6

Interval Since Last Report:          64921255 sec
Crashes Since Last Report:           8432
Per-App Interval Since Last Report:  481826 sec
Per-App Crashes Since Last Report:   13
Anonymous UUID:                      51303DFF-5522-4A62-A203-393F263F4478

Exception Type:  EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000000
Crashed Thread:  0  Dispatch queue: com.apple.main-thread

Thread 0 Crashed:  Dispatch queue: com.apple.main-thread
0   com.yourcompany.MetaPathways2   0x00000001000f9f01 HTree::getTreeDepth() + 1
1   com.yourcompany.MetaPathways2   0x00000001000da4e7 SelectSamples::sendSelection() + 183
2   QtCore                          0x0000000100a74fae QMetaObject::activate(QObject*, QMetaObject const*, int, void**) + 1566
3   QtCore                          0x0000000100a74fae QMetaObject::activate(QObject*, QMetaObject const*, int, void**) + 1566
4   QtGui                           0x00000001013c84f1 QAbstractButton::clicked(bool) + 49
5   QtGui                           0x00000001010ebdb0 QAbstractButton::mousePressEvent(QMouseEvent*) + 208
6   QtGui                           0x00000001010ecfea QAbstractButton::keyPressEvent(QKeyEvent*) + 778
7   QtGui                           0x00000001010ed241 QAbstractButton::mouseReleaseEvent(QMouseEvent*) + 113
8   QtGui                           0x0000000100da0761 QWidget::event(QEvent*) + 2369
9   QtGui                           0x00000001010ec038 QAbstractButton::event(QEvent*) + 40
10  QtGui                           0x0000000101187bb5 QPushButton::event(QEvent*) + 69
11  QtGui                           0x0000000100d4894d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 189
12  QtGui                           0x0000000100d4f4f0 QApplication::notify(QObject*, QEvent*) + 2384
13  QtCore                          0x0000000100a5cb9c QCoreApplication::notifyInternal(QObject*, QEvent*) + 124
14  QtGui                           0x0000000100d4cf3d QApplicationPrivate::sendMouseEvent(QWidget*, QMouseEvent*, QWidget*, QWidget*, QWidget**, QPointer<QWidget>&, bool) + 333
15  QtGui                           0x0000000100cfc9eb QMacCocoaAutoReleasePool::~QMacCocoaAutoReleasePool() + 18939
16  com.apple.AppKit                0x00007fff86965431 -[NSWindow sendEvent:] + 5547
17  QtGui                           0x0000000100ce9577 QWidget::grabMouse(QCursor const&) + 3895
18  com.apple.AppKit                0x00007fff8689aafa -[NSApplication sendEvent:] + 4719
19  QtGui                           0x0000000100cf6b64 QMacInputContext::reset() + 45540
20  com.apple.AppKit                0x00007fff868316de -[NSApplication run] + 474
21  QtGui                           0x0000000100d019a0 QDesktopWidget::resizeEvent(QResizeEvent*) + 13040
22  QtCore                          0x0000000100a5baa4 QEventLoop::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 68
23  QtCore                          0x0000000100a5be54 QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 324
24  QtCore                          0x0000000100a5e53c QCoreApplication::exec() + 188
25  com.yourcompany.MetaPathways2   0x00000001000061e7 main + 199
26  com.yourcompany.MetaPathways2   0x00000001000060f8 start + 52

Thread 1:  Dispatch queue: com.apple.libdispatch-manager
0   libSystem.B.dylib               0x00007fff80346c0a kevent + 10
1   libSystem.B.dylib               0x00007fff80348add _dispatch_mgr_invoke + 154
2   libSystem.B.dylib               0x00007fff803487b4 _dispatch_queue_invoke + 185
3   libSystem.B.dylib               0x00007fff803482de _dispatch_worker_thread2 + 252
4   libSystem.B.dylib               0x00007fff80347c08 _pthread_wqthread + 353
5   libSystem.B.dylib               0x00007fff80347aa5 start_wqthread + 13

Thread 2:  com.apple.CFSocket.private
0   libSystem.B.dylib               0x00007fff80371932 select$DARWIN_EXTSN + 10
1   com.apple.CoreFoundation        0x00007fff83120468 __CFSocketManager + 824
2   libSystem.B.dylib               0x00007fff80366fd6 _pthread_start + 331
3   libSystem.B.dylib               0x00007fff80366e89 thread_start + 13

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x0000000000000000  rbx: 0x0000000106606be0  rcx: 0x000000012a9a8b80  rdx: 0x0000000000000000
  rdi: 0x0000000000000000  rsi: 0x0000000000000001  rbp: 0x00007fff5fbfe500  rsp: 0x00007fff5fbfe170
   r8: 0x0000000000000000   r9: 0x0000000013c0b155  r10: 0x0000000000000001  r11: 0x0000000000000010
  r12: 0x00007fff5fbfe3b0  r13: 0x0000000000000003  r14: 0x0000000000000000  r15: 0x0000000139d3a420
  rip: 0x00000001000f9f01  rfl: 0x0000000000010246  cr2: 0x0000000000000000

Binary Images:
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       0x100233000 -        0x1005c0fff +QtDeclarative 4.8.3 (compatibility 4.8.0) <483EA044-31A6-6AB5-9C55-762F62FD155D> /Applications/MetaPathways2.app/Contents/Frameworks/QtDeclarative.framework/Versions/4/QtDeclarative
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       0x101e35000 -        0x101f76fe7 +QtNetwork 4.8.3 (compatibility 4.8.0) <0710A328-F527-1535-E578-C9BEBFBD459A> /Applications/MetaPathways2.app/Contents/Frameworks/QtNetwork.framework/Versions/4/QtNetwork
       0x105e9c000 -        0x105ea2ff7 +libqgif.dylib ??? (???) <072F0B85-4C27-41F1-B362-4BE31B9E1F41> /Applications/MetaPathways2.app/Contents/PlugIns/imageformats/libqgif.dylib
       0x105ea6000 -        0x105eacff7 +libqico.dylib ??? (???) <432FC194-8BDA-308D-334D-638E85B6CD13> /Applications/MetaPathways2.app/Contents/PlugIns/imageformats/libqico.dylib
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       0x105ef1000 -        0x105ef5ff7 +libqsvg.dylib ??? (???) <3AB942ED-07B3-8692-26DF-FF5FFB90E201> /Applications/MetaPathways2.app/Contents/PlugIns/imageformats/libqsvg.dylib
       0x12752d000 -        0x127581fe7 +libqmng.dylib ??? (???) <683C8CF4-74C7-6D9E-E53B-12D25D7EB7B9> /Applications/MetaPathways2.app/Contents/PlugIns/imageformats/libqmng.dylib
       0x127589000 -        0x1275c6fe7 +QtXml 4.8.3 (compatibility 4.8.0) <36AEDD15-0514-3A6E-AFF7-E4D5BE519AE9> /Applications/MetaPathways2.app/Contents/Frameworks/QtXml.framework/Versions/4/QtXml
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       0x127700000 -        0x127755fe7 +libqtiff.dylib ??? (???) <DBE13CAC-204F-0BAE-D646-698097D9151A> /Applications/MetaPathways2.app/Contents/PlugIns/imageformats/libqtiff.dylib
       0x128c0b000 -        0x128c0efef  libLatinSuppConverter.dylib 49.0.0 (compatibility 1.0.0) <F78219BF-F487-1BB9-6B3E-F479B6401D34> /System/Library/CoreServices/Encodings/libLatinSuppConverter.dylib
    0x7fff5fc00000 -     0x7fff5fc3be0f  dyld 132.1 (???) <29DECB19-0193-2575-D838-CF743F0400B2> /usr/lib/dyld
    0x7fff80003000 -     0x7fff80008ff7  com.apple.CommonPanels 1.2.4 (91) <4D84803B-BD06-D80E-15AE-EFBE43F93605> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/CommonPanels.framework/Versions/A/CommonPanels
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    0x7fff877d6000 -     0x7fff877dcff7  com.apple.CommerceCore 1.0 (9.1) <3691E9BA-BCF4-98C7-EFEC-78DA6825004E> /System/Library/PrivateFrameworks/CommerceKit.framework/Versions/A/Frameworks/CommerceCore.framework/Versions/A/CommerceCore
    0x7fff877dd000 -     0x7fff87829fff  libauto.dylib ??? (???) <F7221B46-DC4F-3153-CE61-7F52C8C293CF> /usr/lib/libauto.dylib
    0x7fff87852000 -     0x7fff87854fff  libRadiance.dylib ??? (???) <BF694EE5-6FDA-553A-CC89-F7135618E9C7> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libRadiance.dylib
    0x7fff87855000 -     0x7fff87920fff  ColorSyncDeprecated.dylib 4.6.0 (compatibility 1.0.0) <86982FBB-B224-CBDA-A9AD-8EE97BDB8681> /System/Library/Frameworks/ApplicationServices.framework/Frameworks/ColorSync.framework/Versions/A/Resources/ColorSyncDeprecated.dylib
    0x7fff87921000 -     0x7fff879d6fe7  com.apple.ink.framework 1.3.3 (107) <8C36373C-5473-3A6A-4972-BC29D504250F> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Ink.framework/Versions/A/Ink
    0x7fff879d7000 -     0x7fff87a8dff7  libobjc.A.dylib 227.0.0 (compatibility 1.0.0) <03140531-3B2D-1EBA-DA7F-E12CC8F63969> /usr/lib/libobjc.A.dylib
    0x7fff87a8e000 -     0x7fff87aa2ff7  com.apple.speech.synthesis.framework 3.10.35 (3.10.35) <621B7415-A0B9-07A7-F313-36BEEDD7B132> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/SpeechSynthesis.framework/Versions/A/SpeechSynthesis
    0x7fff87ba8000 -     0x7fff883b2fe7  libBLAS.dylib 219.0.0 (compatibility 1.0.0) <FC941ECB-71D0-FAE3-DCBF-C5A619E594B8> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
    0x7fff883b3000 -     0x7fff88430fef  libstdc++.6.dylib 7.9.0 (compatibility 7.0.0) <35ECA411-2C08-FD7D-11B1-1B7A04921A5C> /usr/lib/libstdc++.6.dylib
    0x7fff8843d000 -     0x7fff88480fef  libtidy.A.dylib ??? (???) <2F4273D3-418B-668C-F488-7E659D3A8C23> /usr/lib/libtidy.A.dylib
    0x7fff88624000 -     0x7fff88a67fef  libLAPACK.dylib 219.0.0 (compatibility 1.0.0) <0CC61C98-FF51-67B3-F3D8-C5E430C201A9> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
    0x7fff88c8b000 -     0x7fff88cd6fef  com.apple.ImageCaptureCore 1.1 (1.1) <F23CA537-4F18-76FC-8D9C-ED6E645186FC> /System/Library/Frameworks/ImageCaptureCore.framework/Versions/A/ImageCaptureCore
    0x7fff88d1a000 -     0x7fff88d9fff7  com.apple.print.framework.PrintCore 6.3 (312.7) <CDFE82DD-D811-A091-179F-6E76069B432D> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/PrintCore.framework/Versions/A/PrintCore
    0x7fff88da0000 -     0x7fff88defff7  com.apple.DirectoryService.PasswordServerFramework 6.1 (6.1) <0731C40D-71EF-B417-C83B-54C3527A36EA> /System/Library/PrivateFrameworks/PasswordServer.framework/Versions/A/PasswordServer
    0x7fff88df0000 -     0x7fff88f25fff  com.apple.audio.toolbox.AudioToolbox 1.6.7 (1.6.7) <F4814A13-E557-59AF-30FF-E62929367933> /System/Library/Frameworks/AudioToolbox.framework/Versions/A/AudioToolbox
    0x7fff88f26000 -     0x7fff88f2aff7  libmathCommon.A.dylib 315.0.0 (compatibility 1.0.0) <95718673-FEEE-B6ED-B127-BCDBDB60D4E5> /usr/lib/system/libmathCommon.A.dylib
    0x7fff88f2b000 -     0x7fff88f95fe7  libvMisc.dylib 268.0.1 (compatibility 1.0.0) <AF0EA96D-000F-8C12-B952-CB7E00566E08> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvMisc.dylib
    0x7fff88f96000 -     0x7fff88fa5fef  com.apple.opengl 1.6.14 (1.6.14) <ECAE2D12-5BE3-46E7-6EE5-563B80B32A3E> /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
    0x7fff88fa6000 -     0x7fff88fbafff  libGL.dylib ??? (???) <2ECE3B0F-39E1-3938-BF27-7205C6D0358B> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
    0x7fff88fbb000 -     0x7fff88fc1fff  libCGXCoreImage.A.dylib 545.0.0 (compatibility 64.0.0) <D2F8C7E3-CBA1-2E66-1376-04AA839DABBB> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/Resources/libCGXCoreImage.A.dylib
    0x7fff88fc2000 -     0x7fff8907bfff  libsqlite3.dylib 9.6.0 (compatibility 9.0.0) <2C5ED312-E646-9ADE-73A9-6199A2A43150> /usr/lib/libsqlite3.dylib
    0x7fff8907c000 -     0x7fff89585ff7  com.apple.RawCamera.bundle 3.14.0 (646) <75A96BFC-1832-808B-F430-C4C9379C5A98> /System/Library/CoreServices/RawCamera.bundle/Contents/MacOS/RawCamera
    0x7fff89586000 -     0x7fff89589ff7  com.apple.securityhi 4.0 (36638) <AEF55AF1-54D3-DB8D-27A7-E16192E0045A> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/SecurityHI.framework/Versions/A/SecurityHI
    0x7fff8958a000 -     0x7fff895c8fe7  libFontRegistry.dylib ??? (???) <395D7C0D-36B5-B353-0DC8-51ABC0B1C030> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontRegistry.dylib
    0x7fff89ed7000 -     0x7fff89eddff7  IOSurface ??? (???) <8E302BB2-0704-C6AB-BD2F-C2A6C6A2E2C3> /System/Library/Frameworks/IOSurface.framework/Versions/A/IOSurface
    0x7fff89ede000 -     0x7fff89fb2fe7  com.apple.CFNetwork 454.12.4 (454.12.4) <C83E2BA1-1818-B3E8-5334-860AD21D1C80> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CFNetwork.framework/Versions/A/CFNetwork
    0x7fff89fb3000 -     0x7fff8a0bdff7  com.apple.MeshKitIO 1.1 (49.2) <C19D0CCD-1DCB-7EDE-76FA-BF74079AFC6A> /System/Library/PrivateFrameworks/MeshKit.framework/Versions/A/Frameworks/MeshKitIO.framework/Versions/A/MeshKitIO
    0x7fff8a268000 -     0x7fff8a4f1ff7  com.apple.security 6.1.2 (55002) <D224882B-D57B-83AF-3781-548BCEACB327> /System/Library/Frameworks/Security.framework/Versions/A/Security
    0x7fff8a5d8000 -     0x7fff8a5d9ff7  com.apple.TrustEvaluationAgent 1.1 (1) <5952A9FA-BC2B-16EF-91A7-43902A5C07B6> /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent
    0x7fff8a5da000 -     0x7fff8a5f1fff  com.apple.ImageCapture 6.1 (6.1) <79AB2131-2A6C-F351-38A9-ED58B25534FD> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ImageCapture.framework/Versions/A/ImageCapture
    0x7fff8a5f2000 -     0x7fff8a62cfff  libcups.2.dylib 2.8.0 (compatibility 2.0.0) <4F2A4397-89BD-DEAC-4971-EE838FFA0964> /usr/lib/libcups.2.dylib
    0x7fff8a62d000 -     0x7fff8a674fff  com.apple.QuickLookFramework 2.3 (327.7) <A8169A96-FAE6-26B2-A9A9-C78BA5787146> /System/Library/Frameworks/QuickLook.framework/Versions/A/QuickLook
    0x7fff8a675000 -     0x7fff8a680ff7  com.apple.speech.recognition.framework 3.11.1 (3.11.1) <3D65E89B-FFC6-4AAF-D5CC-104F967C8131> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/SpeechRecognition.framework/Versions/A/SpeechRecognition
    0x7fff8a681000 -     0x7fff8a6acff7  libxslt.1.dylib 3.24.0 (compatibility 3.0.0) <3630A97F-55C1-3F34-CA63-3847653C9645> /usr/lib/libxslt.1.dylib
    0x7fff8a6c9000 -     0x7fff8a6f1fff  com.apple.DictionaryServices 1.1.2 (1.1.2) <E9269069-93FA-2B71-F9BA-FDDD23C4A65E> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/DictionaryServices.framework/Versions/A/DictionaryServices
    0x7fff8a6f2000 -     0x7fff8a700ff7  libkxld.dylib ??? (???) <8145A534-95CC-9F3C-B78B-AC9898F38C6F> /usr/lib/system/libkxld.dylib
    0x7fff8a701000 -     0x7fff8a817ff7  libxml2.2.dylib 10.3.0 (compatibility 10.0.0) <3814FCF9-92B9-A6AB-E76A-F7021894AA3F> /usr/lib/libxml2.2.dylib
    0x7fff8a824000 -     0x7fff8a8b1fff  com.apple.iLifeMediaBrowser 2.5.5 (468.2.2) <0A7B422E-5D79-9980-2477-05DC2CB5CF7C> /System/Library/PrivateFrameworks/iLifeMediaBrowser.framework/Versions/A/iLifeMediaBrowser
    0x7fffffe00000 -     0x7fffffe01fff  libSystem.B.dylib ??? (???) <9AB4F1D1-89DC-0E8A-DC8E-A4FE4D69DB69> /usr/lib/libSystem.B.dylib

A user is unable to provide input and output folders via the browse button.
Nothing occurs when they click the buttons.

I had to delete the old preferences files in ~/Library/Preferences in order to get the new installation going (probably just an incompatibility between the .plist file versions).

Maybe just delete the old pref. files or let the user know of this issue? Took me a while to figure this out.

Mac OS 10.6.8
Previous MP installation: 2.0