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Dear Bio-Linux Users,<br>
<br>
maybe you're able to help me with the following problem:<br>
Anytime I try to use "<b>filter_fasta.py</b>" (<b>qiime package</b>)
I get an error message.<br>
<br>
qiime > filter_fasta.py -f data.fas -o test -s
list <br>
Traceback (most recent call last):<br>
File "/usr/local/bin/filter_fasta.py", line 183, in <module><br>
main()<br>
File "/usr/local/bin/filter_fasta.py", line 180, in main<br>
negate)<br>
File "/usr/local/bin/filter_fasta.py", line 84, in filter_fasta_fp<br>
return filter_fasta(input_seqs,output_f,seqs_to_keep,negate)<br>
File "/usr/lib/python2.7/dist-packages/qiime/filter.py", line 352,
in filter_fasta<br>
for seq_id, seq in parse_fasta(input_seqs_f):<br>
File
"/usr/lib/python2.7/dist-packages/skbio/parse/sequences/fasta.py",
line 136, in parse_fasta<br>
for rec in finder(infile):<br>
File
"/usr/lib/python2.7/dist-packages/skbio/parse/record_finder.py",
line 150, in parser<br>
line = constructor(l)<br>
TypeError: descriptor 'strip' requires a 'str' object but received a
'tuple'<br>
<br>
I'm not sure if it is really a qiime-related error. Maybe something
went wrong with the installation. However, I already re-installed
the whole qiime package once and there seems to be no problem
(output from "print_qiime_config_all" see below).<br>
<br>
Is there anyone who is able to help me with this issue?<br>
<br>
Thanks a lot,<br>
<br>
best regards,<br>
Marvin<br>
<br>
<br>
<br>
<br>
print_qiime_config_all:<br>
System information<br>
==================<br>
Platform: linux2<br>
Python version: 2.7.6 (default, Jun 22 2015, 17:58:13) [GCC
4.8.2]<br>
Python executable: /usr/bin/python<br>
<br>
QIIME default reference information<br>
===================================<br>
For details on what files are used as QIIME's default references,
see here:<br>
<a class="moz-txt-link-freetext" href="https://github.com/biocore/qiime-default-reference/releases/tag/0.1.1">https://github.com/biocore/qiime-default-reference/releases/tag/0.1.1</a><br>
<br>
Dependency versions<br>
===================<br>
QIIME library version: 1.9.0<br>
QIIME script version: 1.9.0+dfsg-0biolinux5<br>
qiime-default-reference version: 0.1.1<br>
NumPy version: 1.8.2<br>
SciPy version: 0.13.3<br>
pandas version: 0.13.1<br>
matplotlib version: 1.3.1<br>
biom-format version: 2.1.4<br>
h5py version: 2.2.1 (HDF5 version: 1.8.11)<br>
qcli version: 0.1.0<br>
pyqi version: 0.3.2<br>
scikit-bio version: 0.2.3<br>
PyNAST version: 1.2.2<br>
Emperor version: 0.9.51<br>
burrito version: 0.9.0<br>
burrito-fillings version: Installed.<br>
sortmerna version: SortMeRNA version 2.0,
29/11/2014<br>
sumaclust version: SUMACLUST Version 1.0.01<br>
swarm version: Swarm 1.2.20 [Feb 1 2015
09:42:15]<br>
gdata: Not installed.<br>
<br>
QIIME config values<br>
===================<br>
For definitions of these settings and to learn how to configure
QIIME, see here:<br>
<a class="moz-txt-link-freetext" href="http://qiime.org/install/qiime_config.html">http://qiime.org/install/qiime_config.html</a><br>
<a class="moz-txt-link-freetext" href="http://qiime.org/tutorials/parallel_qiime.html">http://qiime.org/tutorials/parallel_qiime.html</a><br>
<br>
blastmat_dir: /usr/share/ncbi/data<br>
cluster_jobs_fp: None<br>
pick_otus_reference_seqs_fp:
/usr/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta<br>
jobs_to_start: 1<br>
pynast_template_alignment_blastdb: None<br>
qiime_scripts_dir: /usr/lib/qiime/bin/<br>
working_dir: .<br>
pynast_template_alignment_fp:
/usr/share/qiime/data/core_set_aligned.fasta.imputed<br>
python_exe_fp: python<br>
temp_dir: /tmp<br>
assign_taxonomy_reference_seqs_fp: #
/usr/share/qiime/data/gg_13_8_otus/rep_set/97_otus.fasta<br>
blastall_fp: blastall<br>
seconds_to_sleep: 60<br>
assign_taxonomy_id_to_taxonomy_fp: #
/usr/share/qiime/data/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt<br>
<br>
QIIME base install test results<br>
===============================<br>
.........<br>
----------------------------------------------------------------------<br>
Ran 9 tests in 0.027s<br>
<br>
OK<br>
<br>
Here are the versions of the packages that QIIME depends on as
reported by<br>
the system package manager:<br>
<br>
ampliconnoise : 1.29-2<br>
blast2 : 1:2.2.26.20120620-7<br>
bwa : 0.7.12-0biolinux1<br>
cd-hit : 4.6.1-2012-08-27-2<br>
chimeraslayer : 20101212+dfsg-1<br>
clearcut : 1.0.9-0biolinux1.1<br>
clustalw : 2.1+lgpl-4<br>
ea-utils : 1.1.2+dfsg-1biolinux1<br>
emperor : 0.9.51-0biolinux1<br>
fasttree : 2.1.7-1biolinux1.1<br>
infernal : 1.1.1-2ubuntu1<br>
mafft : 7.215-0biolinux1<br>
mothur : 1.34.4+repack-0biolinux1<br>
muscle : 1:3.8.31-1<br>
parsinsert : 1.04-1biolinux1.1<br>
pynast : 1.2.2-0biolinux1.1<br>
python : 2.7.5-5ubuntu3<br>
python-biom-format : 2.1.4-0biolinux2<br>
python-burrito : 0.9.0-0biolinux3<br>
python-burrito-fillings : 0.1.0-0biolinux4<br>
python-cogent : 1.5.3-2biolinux2<br>
python-matplotlib : 1.3.1-1ubuntu5<br>
python-mpi4py : 1.3.1+hg20131106-1build3<br>
python-numpy : 1:1.8.2-0ubuntu0.1<br>
python-pandas : 0.13.1-2ubuntu2<br>
python-qcli : 0.1.0-1<br>
python : 2.7.5-5ubuntu3<br>
qiime-data : 1.9.0+dfsg-0biolinux5<br>
qiime-default-reference : 0.1.1-0biolinux2<br>
r-cran-optparse : 1.3.0-1cran1ppa0<br>
raxml : 8.0.26-0biolinux1<br>
rdp-classifier : 2.10.2+dfsg-0biolinux1<br>
seqprep : 1.1-0biolinux2<br>
sortmerna : 2.0-0biolinux1<br>
sumatra : 1.0.01-0ubuntu1<br>
swarm : 1.2.20-0biolinux1<br>
vsearch : 1.1.1.nodata-0biolinux1<br>
<br>
OK<br>
<br>
<br>
<pre class="moz-signature" cols="72">--
Dipl. Biol. Marvin Djukic
Georg-August Universität Göttingen
Institut für Mikrobiologie und Genetik
Göttingen Genomics Laboratory
Grisebachstraße 8
37077 Göttingen
Germany
Tel. 0049-(0)551-39-33843
Mobil: 0176-45743636
E-Mail: <a class="moz-txt-link-abbreviated" href="mailto:mdjukic1@gwdg.de">mdjukic1@gwdg.de</a>
<a class="moz-txt-link-freetext" href="http://appmibio.uni-goettingen.de">http://appmibio.uni-goettingen.de</a></pre>
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