-
Notifications
You must be signed in to change notification settings - Fork 3.3k
/
build_failure.osx-64.yaml
105 lines (104 loc) · 7.56 KB
/
build_failure.osx-64.yaml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
recipe_sha: 65e7d2e1e37f5d09b369b83c2b28d55d132f52dfa10e858233a874f106158aa3 # The hash of the recipe's meta.yaml at which this recipe failed to build.
skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
category: test failure
log: |2-
libzlib: 1.3.1-h87427d6_1 conda-forge
llvm-openmp: 18.1.7-h15ab845_0 conda-forge
mafft: 7.526-hec52a4b_0 conda-forge
mpfr: 4.2.1-h4f6b447_1 conda-forge
muscle: 3.8.1551-hb280591_6 bioconda
ncurses: 6.5-h5846eda_0 conda-forge
openjdk: 22.0.1-h2d185b6_0 conda-forge
openssl: 3.3.1-h87427d6_0 conda-forge
pasta: 1.9.0-py311h29d3010_1 local
pcre: 8.45-he49afe7_0 conda-forge
prank: 170427-h85dcccf_0 bioconda
pymongo: 4.7.3-py311hbafa61a_0 conda-forge
python: 3.11.9-h657bba9_0_cpython conda-forge
python_abi: 3.11-4_cp311 conda-forge
raxml: 8.2.13-h2413b67_1 bioconda
readline: 8.2-h9e318b2_1 conda-forge
sniffio: 1.3.1-pyhd8ed1ab_0 conda-forge
tk: 8.6.13-h1abcd95_1 conda-forge
tzdata: 2024a-h0c530f3_0 conda-forge
xz: 5.2.6-h775f41a_0 conda-forge
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
clustalw2 -help
grep OPTIONS
hmmalign -h
grep HMMER
hmmbuild -h
grep HMMER
muscle -version
grep -i MUSCLE
prank -help
grep prank
raxml -h
grep -i raxml
raxmlp -h
grep -i raxml
export PASTA_LOGGING_LEVEL=DEBUG
PASTA_LOGGING_LEVEL=DEBUG
export PASTA_LOGGING_FORMAT=RICH
PASTA_LOGGING_FORMAT=RICH
run_pasta.py -i /opt/mambaforge/envs/bioconda/conda-bld/pasta_1718123761694/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/share/pasta/data/small.fasta
PASTA ERROR: PASTA is exiting because of an error:
invalid mode: 'rU'
WARNING: Tests failed for pasta-1.9.0-py311h29d3010_1.tar.bz2 - moving package to /opt/mambaforge/envs/bioconda/conda-bld/broken
TESTS FAILED: pasta-1.9.0-py311h29d3010_1.tar.bz2
export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/pasta_1718123761694/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla
export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/pasta_1718123761694/test_tmp
import: 'pasta'
import: 'pasta'
-OPTIONS :list the command line parameters
# HMMER 3.1b2 (February 2015); http://hmmer.org/
# HMMER 3.1b2 (February 2015); http://hmmer.org/
MUSCLE v3.8.1551 by Robert C. Edgar
prank v.170427. Minimal usage: 'prank sequence_file'
Advanced usage: 'prank [optional parameters] -d=sequence_file [optional parameters]'
This is RAxML version 8.2.12 released by Alexandros Stamatakis on May 2018.
Please also consult the RAxML-manual
Please report bugs via the RAxML google group!
raxmlHPC[-SSE3|-AVX|-PTHREADS|-PTHREADS-SSE3|-PTHREADS-AVX|-HYBRID|-HYBRID-SSE3|HYBRID-AVX]
-A Specify one of the secondary structure substitution models implemented in RAxML.
-c Specify number of distinct rate catgories for RAxML when model of rate heterogeneity
"-f c": check if the alignment can be properly read by RAxML
in the two tree files. A file called RAxML_bipartitionFrequencies.outpuFileName
you will need to start RAxML with a non-comprehensive reference tree and an alignment containing all sequences (reference query)
you will need to start RAxML with a non-comprehensive reference tree and an alignment containing all sequences (reference query)
you will need to start RAxML with a non-comprehensive reference tree and an alignment containing all sequences (reference query)
-K Specify one of the multi-state substitution models (max 32 states) implemented in RAxML.
with RAxML using the -f e tree evaluation option. The file name should be:
RAxML_binaryModelParameters.runID
-w FULL (!) path to the directory into which RAxML shall write its output files
CAUTION: unlike in version 7.0.4 RAxML will conduct rapid BS replicates under
RAxML will only do a randomized stepwise addition order parsimony tree reconstruction
-y If you want to only compute a parsimony starting tree with RAxML specify "-y",
--flag-check When using this option, RAxML will only check if all command line flags specifed are available and then exit
RAxML will test all available prot subst. models except for LG4M, LG4X and GTR-based models, with and without empirical base frequencies.
--print-identical-sequences specify that RAxML shall automatically generate a .reduced alignment with all
This is RAxML version 8.2.12 released by Alexandros Stamatakis on May 2018.
Please also consult the RAxML-manual
Please report bugs via the RAxML google group!
raxmlHPC[-SSE3|-AVX|-PTHREADS|-PTHREADS-SSE3|-PTHREADS-AVX|-HYBRID|-HYBRID-SSE3|HYBRID-AVX]
-A Specify one of the secondary structure substitution models implemented in RAxML.
-c Specify number of distinct rate catgories for RAxML when model of rate heterogeneity
"-f c": check if the alignment can be properly read by RAxML
in the two tree files. A file called RAxML_bipartitionFrequencies.outpuFileName
you will need to start RAxML with a non-comprehensive reference tree and an alignment containing all sequences (reference query)
you will need to start RAxML with a non-comprehensive reference tree and an alignment containing all sequences (reference query)
you will need to start RAxML with a non-comprehensive reference tree and an alignment containing all sequences (reference query)
-K Specify one of the multi-state substitution models (max 32 states) implemented in RAxML.
with RAxML using the -f e tree evaluation option. The file name should be:
RAxML_binaryModelParameters.runID
-w FULL (!) path to the directory into which RAxML shall write its output files
CAUTION: unlike in version 7.0.4 RAxML will conduct rapid BS replicates under
RAxML will only do a randomized stepwise addition order parsimony tree reconstruction
-y If you want to only compute a parsimony starting tree with RAxML specify "-y",
--flag-check When using this option, RAxML will only check if all command line flags specifed are available and then exit
RAxML will test all available prot subst. models except for LG4M, LG4X and GTR-based models, with and without empirical base frequencies.
--print-identical-sequences specify that RAxML shall automatically generate a .reduced alignment with all
PASTA INFO: Reading input sequences from '$PREFIX/share/pasta/data/small.fasta'...
# Last 100 lines of the build log.