Hi,
I am trying to run uclust with pick_otus.py command but have been getting the following error:
Traceback (most recent call last):
File "/usr/lib/qiime/bin/pick_otus.py", line 999, in <module>
main()
File "/usr/lib/qiime/bin/pick_otus.py", line 787, in main
result_path=result_path, log_path=log_path, HALT_EXEC=False)
File "/usr/lib/python2.7/dist-packages/qiime/pick_otus.py", line 1286, in __call__
HALT_EXEC=HALT_EXEC)
File "/usr/lib/python2.7/dist-packages/bfillings/uclust.py", line 583, in get_clusters_from_fasta_filepath
raise ApplicationError('Error running uclust. Possible causes are '
burrito.util.ApplicationError: Error running uclust. Possible causes are unsupported version (current supported version is v1.2.22) is installed or improperly formatted input file was provided
However, I have run 'validate_demultiplexed_fasta.py' and found no issues with my input file, and I think my uclust installation is correct:
$ qiime > uclust --version
uclust v1.2.22q
$ qiime > which uclust
/usr/bin/uclust
I have also tried clustering the reads directly with "usearch -cluster_fast" (32-bit version), and had no issue, which leads me to believe this is not a memory issue (although I could be wrong?). My input fasta file is only 68Mb.
The results of print_qiime_config.py -t are below:
System information
==================
Platform: linux2
Python version: 2.7.6 (default, Mar 22 2014, 22:59:56) [GCC 4.8.2]
Python executable: /usr/bin/python
QIIME default reference information
===================================
For details on what files are used as QIIME's default references, see here:
https://github.com/biocore/qiime-default-reference/releases/tag/0.1.1Dependency versions
===================
QIIME library version: 1.9.0
QIIME script version: 1.9.0+dfsg-0biolinux5
qiime-default-reference version: 0.1.1
NumPy version: 1.8.2
SciPy version: 0.13.3
pandas version: 0.13.1
matplotlib version: 1.3.1
biom-format version: 2.1.4
h5py version: 2.2.1 (HDF5 version: 1.8.11)
qcli version: 0.1.0
pyqi version: 0.3.2
scikit-bio version: 0.2.3
PyNAST version: 1.2.2
Emperor version: 0.9.51
burrito version: 0.9.0
burrito-fillings version: Installed.
sortmerna version: SortMeRNA version 2.0, 29/11/2014
sumaclust version: SUMACLUST Version 1.0.01
swarm version: Swarm 1.2.20 [Feb 1 2015 09:42:15]
gdata: Not installed.
QIIME config values
===================
For definitions of these settings and to learn how to configure QIIME, see here:
http://qiime.org/install/qiime_config.html http://qiime.org/tutorials/parallel_qiime.html blastmat_dir: /usr/share/ncbi/data
cluster_jobs_fp: None
pick_otus_reference_seqs_fp: /usr/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
jobs_to_start: 1
pynast_template_alignment_blastdb: None
qiime_scripts_dir: /usr/lib/qiime/bin/
working_dir: .
pynast_template_alignment_fp: /usr/share/qiime/data/core_set_aligned.fasta.imputed
python_exe_fp: python
temp_dir: /tmp
assign_taxonomy_reference_seqs_fp: # /usr/share/qiime/data/gg_13_8_otus/rep_set/97_otus.fasta
blastall_fp: blastall
seconds_to_sleep: 60
assign_taxonomy_id_to_taxonomy_fp: # /usr/share/qiime/data/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
QIIME base install test results
===============================
.........
----------------------------------------------------------------------
Ran 9 tests in 0.015s
OK
Apologies for posting when there are a few similar questions here already- however, none of them have helped me solve this issue.
Thanks and best,
Caitlin.