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Viewing changes to qiime_test_data/pick_open_reference_otus/ucrss_iter/log_20130409153806.txt

  • Committer: Package Import Robot
  • Author(s): Andreas Tille
  • Date: 2013-06-17 18:28:26 UTC
  • mfrom: (9.1.2 sid)
  • Revision ID: package-import@ubuntu.com-20130617182826-376az5ad080a0sfe
Tags: 1.7.0+dfsg-1
Upload preparations done for BioLinux to Debian

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qiime_test_data/pick_open_reference_otus/ucrss_iter/log_20130409153806.txt
 
1
Logging started at 15:38:06 on 09 Apr 2013
 
2
QIIME version: 1.6.0-dev
 
3
 
 
4
qiime_config values:
 
5
blastmat_dir    /Applications/blast-2.2.22/data/
 
6
sc_queue        all.q
 
7
topiaryexplorer_project_dir     /Users/caporaso/code/TopiaryExplorer-0.9.1/
 
8
pynast_template_alignment_fp    /Users/caporaso/data/greengenes_core_sets/core_set_aligned_imputed.fasta_11_8_07.no_dots
 
9
cluster_jobs_fp start_parallel_jobs.py
 
10
assign_taxonomy_reference_seqs_fp       /Users/caporaso/data/gg_12_10_otus/rep_set/97_otus.fasta
 
11
torque_queue    friendlyq
 
12
template_alignment_lanemask_fp  /Users/caporaso/data/greengenes_core_sets/lanemask_in_1s_and_0s.txt
 
13
jobs_to_start   2
 
14
cloud_environment       False
 
15
qiime_scripts_dir       /Users/caporaso/code/Qiime/scripts
 
16
denoiser_min_per_core   50
 
17
python_exe_fp   python
 
18
temp_dir        /Users/caporaso/temp
 
19
blastall_fp     blastall
 
20
seconds_to_sleep        1
 
21
assign_taxonomy_id_to_taxonomy_fp       /Users/caporaso/data/gg_12_10_otus/taxonomy/97_otu_taxonomy.txt
 
22
 
 
23
parameter file values:
 
24
align_seqs:min_length   75
 
25
parallel:jobs_to_start  2
 
26
pick_otus:enable_rev_strand_match       True
 
27
 
 
28
Input file md5 sums:
 
29
/Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/seqs1.fna: 094e424cf45cba69ef1c45fc7f61366f
 
30
/Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/refseqs.fna: facf235fdcd71d1e99048705276103ab
 
31
 
 
32
Overridding similiary with 0.600.
 
33
Forcing --suppress_new_clusters as this is reference-based OTU picking.
 
34
 
 
35
Forcing --suppress_new_clusters as this is reference-based OTU picking.
 
36
 
 
37
Executing commands.
 
38
 
 
39
# Pick Reference OTUs (prefilter) command 
 
40
pick_otus.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/seqs1.fna -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//prefilter_otus/ -r /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/refseqs.fna -m uclust_ref --similarity 0.6 --enable_rev_strand_match --suppress_new_clusters
 
41
 
 
42
Stdout:
 
43
 
 
44
Stderr:
 
45
 
 
46
# Filter prefilter failures from input command 
 
47
filter_fasta.py -f /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/seqs1.fna -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//prefilter_otus//prefiltered_seqs1.fna -s /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//prefilter_otus//seqs1_failures.txt -n
 
48
 
 
49
Stdout:
 
50
 
 
51
Stderr:
 
52
 
 
53
# Pick Reference OTUs command 
 
54
pick_otus.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//prefilter_otus//prefiltered_seqs1.fna -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//step1_otus -r /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/refseqs.fna -m uclust_ref --enable_rev_strand_match --suppress_new_clusters
 
55
 
 
56
Stdout:
 
57
 
 
58
Stderr:
 
59
 
 
60
# Generate full failures fasta file command 
 
61
filter_fasta.py -f /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//prefilter_otus//prefiltered_seqs1.fna -s /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//step1_otus/prefiltered_seqs1_failures.txt -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//step1_otus/failures.fasta
 
62
 
 
63
Stdout:
 
64
 
 
65
Stderr:
 
66
 
 
67
Forcing --suppress_new_clusters as this is reference-based OTU picking.
 
68
 
 
69
Executing commands.
 
70
 
 
71
# Pick rep set command 
 
72
pick_rep_set.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//step1_otus/prefiltered_seqs1_otus.txt -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//step1_otus/step1_rep_set.fna -f /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//prefilter_otus//prefiltered_seqs1.fna
 
73
 
 
74
Stdout:
 
75
 
 
76
Stderr:
 
77
 
 
78
# Pick de novo OTUs for new clusters command 
 
79
pick_otus.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//step1_otus/subsampled_failures.fasta -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//step2_otus/ -m uclust  --uclust_otu_id_prefix New.0.ReferenceOTU --enable_rev_strand_match
 
80
 
 
81
Stdout:
 
82
 
 
83
Stderr:
 
84
 
 
85
# Pick representative set for subsampled failures command 
 
86
pick_rep_set.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//step2_otus//subsampled_failures_otus.txt -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//step2_otus//step2_rep_set.fna -f /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//step1_otus/subsampled_failures.fasta
 
87
 
 
88
Stdout:
 
89
 
 
90
Stderr:
 
91
 
 
92
# Pick reference OTUs using de novo rep set command 
 
93
pick_otus.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//step1_otus/failures.fasta -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//step3_otus/ -r /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//step2_otus//step2_rep_set.fna -m uclust_ref --enable_rev_strand_match --suppress_new_clusters
 
94
 
 
95
Stdout:
 
96
 
 
97
Stderr:
 
98
 
 
99
# Create fasta file of step3 failures command 
 
100
filter_fasta.py -f /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//step1_otus/failures.fasta -s /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//step3_otus//failures_failures.txt -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//step3_otus//failures_failures.fasta
 
101
 
 
102
Stdout:
 
103
 
 
104
Stderr:
 
105
 
 
106
# Pick de novo OTUs on step3 failures command 
 
107
pick_otus.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//step3_otus//failures_failures.fasta -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//step4_otus/ -m uclust  --uclust_otu_id_prefix New.0.CleanUp.ReferenceOTU --enable_rev_strand_match
 
108
 
 
109
Stdout:
 
110
 
 
111
Stderr:
 
112
 
 
113
# Merge OTU maps command 
 
114
cat /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//step1_otus/prefiltered_seqs1_otus.txt /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//step3_otus//failures_otus.txt /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//step4_otus//failures_failures_otus.txt >> /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//final_otu_map.txt
 
115
 
 
116
Stdout:
 
117
 
 
118
Stderr:
 
119
 
 
120
# Pick representative set for subsampled failures command 
 
121
pick_rep_set.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//step4_otus//failures_failures_otus.txt -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//step4_otus//step4_rep_set.fna -f /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//step3_otus//failures_failures.fasta
 
122
 
 
123
Stdout:
 
124
 
 
125
Stderr:
 
126
 
 
127
Executing commands.
 
128
 
 
129
# Make the otu table command 
 
130
make_otu_table.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//final_otu_map_mc2.txt -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//otu_table_mc2.biom
 
131
 
 
132
Stdout:
 
133
 
 
134
Stderr:
 
135
 
 
136
Input file md5 sums:
 
137
/Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/seqs2.fna: 2b339c49ea204172da7f59973de039cc
 
138
/Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//new_refseqs.fna: 20a5adbe7d211c9e07b8a6c2307f0002
 
139
 
 
140
Overridding similiary with 0.600.
 
141
Forcing --suppress_new_clusters as this is reference-based OTU picking.
 
142
 
 
143
Forcing --suppress_new_clusters as this is reference-based OTU picking.
 
144
 
 
145
Executing commands.
 
146
 
 
147
# Pick Reference OTUs (prefilter) command 
 
148
pick_otus.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/seqs2.fna -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//prefilter_otus/ -r /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/refseqs.fna -m uclust_ref --similarity 0.6 --enable_rev_strand_match --suppress_new_clusters
 
149
 
 
150
Stdout:
 
151
 
 
152
Stderr:
 
153
 
 
154
# Filter prefilter failures from input command 
 
155
filter_fasta.py -f /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/seqs2.fna -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//prefilter_otus//prefiltered_seqs2.fna -s /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//prefilter_otus//seqs2_failures.txt -n
 
156
 
 
157
Stdout:
 
158
 
 
159
Stderr:
 
160
 
 
161
# Pick Reference OTUs command 
 
162
pick_otus.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//prefilter_otus//prefiltered_seqs2.fna -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//step1_otus -r /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//new_refseqs.fna -m uclust_ref --enable_rev_strand_match --suppress_new_clusters
 
163
 
 
164
Stdout:
 
165
 
 
166
Stderr:
 
167
 
 
168
# Generate full failures fasta file command 
 
169
filter_fasta.py -f /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//prefilter_otus//prefiltered_seqs2.fna -s /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//step1_otus/prefiltered_seqs2_failures.txt -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//step1_otus/failures.fasta
 
170
 
 
171
Stdout:
 
172
 
 
173
Stderr:
 
174
 
 
175
Forcing --suppress_new_clusters as this is reference-based OTU picking.
 
176
 
 
177
Executing commands.
 
178
 
 
179
# Pick rep set command 
 
180
pick_rep_set.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//step1_otus/prefiltered_seqs2_otus.txt -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//step1_otus/step1_rep_set.fna -f /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//prefilter_otus//prefiltered_seqs2.fna
 
181
 
 
182
Stdout:
 
183
 
 
184
Stderr:
 
185
 
 
186
# Pick de novo OTUs for new clusters command 
 
187
pick_otus.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//step1_otus/subsampled_failures.fasta -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//step2_otus/ -m uclust  --uclust_otu_id_prefix New.1.ReferenceOTU --enable_rev_strand_match
 
188
 
 
189
Stdout:
 
190
 
 
191
Stderr:
 
192
 
 
193
# Pick representative set for subsampled failures command 
 
194
pick_rep_set.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//step2_otus//subsampled_failures_otus.txt -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//step2_otus//step2_rep_set.fna -f /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//step1_otus/subsampled_failures.fasta
 
195
 
 
196
Stdout:
 
197
 
 
198
Stderr:
 
199
 
 
200
# Pick reference OTUs using de novo rep set command 
 
201
pick_otus.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//step1_otus/failures.fasta -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//step3_otus/ -r /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//step2_otus//step2_rep_set.fna -m uclust_ref --enable_rev_strand_match --suppress_new_clusters
 
202
 
 
203
Stdout:
 
204
 
 
205
Stderr:
 
206
 
 
207
# Create fasta file of step3 failures command 
 
208
filter_fasta.py -f /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//step1_otus/failures.fasta -s /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//step3_otus//failures_failures.txt -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//step3_otus//failures_failures.fasta
 
209
 
 
210
Stdout:
 
211
 
 
212
Stderr:
 
213
 
 
214
# Pick de novo OTUs on step3 failures command 
 
215
pick_otus.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//step3_otus//failures_failures.fasta -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//step4_otus/ -m uclust  --uclust_otu_id_prefix New.1.CleanUp.ReferenceOTU --enable_rev_strand_match
 
216
 
 
217
Stdout:
 
218
 
 
219
Stderr:
 
220
 
 
221
# Merge OTU maps command 
 
222
cat /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//step1_otus/prefiltered_seqs2_otus.txt /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//step3_otus//failures_otus.txt /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//step4_otus//failures_failures_otus.txt >> /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//final_otu_map.txt
 
223
 
 
224
Stdout:
 
225
 
 
226
Stderr:
 
227
 
 
228
# Pick representative set for subsampled failures command 
 
229
pick_rep_set.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//step4_otus//failures_failures_otus.txt -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//step4_otus//step4_rep_set.fna -f /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//step3_otus//failures_failures.fasta
 
230
 
 
231
Stdout:
 
232
 
 
233
Stderr:
 
234
 
 
235
Executing commands.
 
236
 
 
237
# Make the otu table command 
 
238
make_otu_table.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//final_otu_map_mc2.txt -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//otu_table_mc2.biom
 
239
 
 
240
Stdout:
 
241
 
 
242
Stderr:
 
243
 
 
244
Executing commands.
 
245
 
 
246
# Merge OTU tables command 
 
247
merge_otu_tables.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//0//otu_table_mc2.biom,/Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//1//otu_table_mc2.biom -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//otu_table_mc2.biom
 
248
 
 
249
Stdout:
 
250
 
 
251
Stderr:
 
252
 
 
253
Executing commands.
 
254
 
 
255
# Assign taxonomy command 
 
256
assign_taxonomy.py -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//rdp_assigned_taxonomy -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//rep_set.fna 
 
257
 
 
258
Stdout:
 
259
 
 
260
Stderr:
 
261
 
 
262
Executing commands.
 
263
 
 
264
# Add taxa to OTU table command 
 
265
add_metadata.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//otu_table_mc2.biom --observation_mapping_fp /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//rdp_assigned_taxonomy/rep_set_tax_assignments.txt -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//otu_table_mc2_w_tax.biom --sc_separated taxonomy --observation_header OTUID,taxonomy
 
266
 
 
267
Stdout:
 
268
 
 
269
Stderr:
 
270
 
 
271
Executing commands.
 
272
 
 
273
# Align sequences command 
 
274
align_seqs.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//rep_set.fna -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//pynast_aligned_seqs --min_length 75
 
275
 
 
276
Stdout:
 
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# Filter alignment command 
 
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filter_alignment.py -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//pynast_aligned_seqs -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//pynast_aligned_seqs/rep_set_aligned.fasta 
 
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# Build phylogenetic tree command 
 
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make_phylogeny.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//pynast_aligned_seqs/rep_set_aligned_pfiltered.fasta -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_iter//rep_set.tre 
 
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Executing commands.
 
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Logging stopped at 15:40:09 on 09 Apr 2013