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February 1, 2013 11:16
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maasha@maxwell:~/data$ unzip qiime_tutorial-v1.5.0.zip | |
Archive: qiime_tutorial-v1.5.0.zip | |
creating: qiime_tutorial-v1.5.0/ | |
creating: qiime_tutorial-v1.5.0/18S_tutorial_files/ | |
inflating: qiime_tutorial-v1.5.0/18S_tutorial_files/18S_tutorial_sample_seqs.fna | |
inflating: qiime_tutorial-v1.5.0/Fasting_Example.fna | |
inflating: qiime_tutorial-v1.5.0/Fasting_Example.qual | |
inflating: qiime_tutorial-v1.5.0/Fasting_Example.sff | |
inflating: qiime_tutorial-v1.5.0/Fasting_Example.sff.txt | |
inflating: qiime_tutorial-v1.5.0/Fasting_Map.txt | |
inflating: qiime_tutorial-v1.5.0/qiime_tutorial_commands_parallel.sh | |
inflating: qiime_tutorial-v1.5.0/qiime_tutorial_commands_serial.sh | |
inflating: qiime_tutorial-v1.5.0/README | |
maasha@maxwell:~/data$ cd qiime_tutorial-v1.5.0 | |
maasha@maxwell:~/data/qiime_tutorial-v1.5.0$ ./ | |
18S_tutorial_files/ qiime_tutorial_commands_parallel.sh qiime_tutorial_commands_serial.sh | |
maasha@maxwell:~/data/qiime_tutorial-v1.5.0$ ./qiime_tutorial_commands_serial.sh | |
Check mapping file | |
Demultiplexing | |
Pick OTUs through OTU table | |
Traceback (most recent call last): | |
File "/home/maasha/install/QIIME1.6/bin/pick_otus_through_otu_table.py", line 131, in <module> | |
main() | |
File "/home/maasha/install/QIIME1.6/bin/pick_otus_through_otu_table.py", line 128, in main | |
status_update_callback=status_update_callback) | |
File "/home/maasha/install/QIIME1.6/lib/python2.7/site-packages/qiime/workflow.py", line 471, in run_pick_otus_through_otu_table | |
close_logger_on_success=close_logger_on_success) | |
File "/home/maasha/install/QIIME1.6/lib/python2.7/site-packages/qiime/workflow.py", line 135, in call_commands_serially | |
raise WorkflowError, msg | |
qiime.workflow.WorkflowError: | |
*** ERROR RAISED DURING STEP: Align sequences | |
Command run was: | |
python /home/maasha/Install/QIIME1.6/bin/align_seqs.py -i otus/rep_set//seqs_rep_set.fasta -o otus/pynast_aligned_seqs | |
Command returned exit status: 1 | |
Stdout: | |
Stderr | |
Traceback (most recent call last): | |
File "/home/maasha/Install/QIIME1.6/bin/align_seqs.py", line 205, in <module> | |
main() | |
File "/home/maasha/Install/QIIME1.6/bin/align_seqs.py", line 188, in main | |
log_path=log_path,failure_path=failure_path) | |
File "/home/maasha/install/QIIME1.6/lib/python2.7/site-packages/qiime/align_seqs.py", line 240, in __call__ | |
aligned=DenseAlignment) | |
File "/home/maasha/install/QIIME1.6/lib/python2.7/site-packages/cogent/__init__.py", line 108, in LoadSeqs | |
label_to_name=label_to_name, **constructor_kw) | |
File "/home/maasha/install/QIIME1.6/lib/python2.7/site-packages/cogent/core/alignment.py", line 1957, in __init__ | |
super(DenseAlignment, self).__init__(*args, **kwargs) | |
File "/home/maasha/install/QIIME1.6/lib/python2.7/site-packages/cogent/core/alignment.py", line 298, in __init__ | |
Alphabet=self.Alphabet) | |
File "/home/maasha/install/QIIME1.6/lib/python2.7/site-packages/cogent/core/alignment.py", line 420, in _names_seqs_order | |
seqs, names = conversion_f(data, Alphabet=Alphabet) | |
File "/home/maasha/install/QIIME1.6/lib/python2.7/site-packages/cogent/core/alignment.py", line 1858, in aln_from_kv_pairs | |
result = array(map(Alphabet.toIndices, seqs), array_type) | |
ValueError: setting an array element with a sequence. |
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