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Hi Tim,<br>
<br>
thanks for your reply. (Now I should be subscribed to the list.)<br>
<br>
I updated Qiime to 1.9.1, but the error is still exactly the same.
I'm also <b>not</b><b> able to run filter_fasta.py with the sample
data set</b>. Same error.<br>
Maybe someone else has an idea. Don't know what to change/do at the
moment. <br>
<br>
Thanks a lot,<br>
regards,<br>
Marvin<br>
<br>
<br>
<div class="moz-cite-prefix">On 31.07.2015 13:02, Tim Booth wrote:<br>
</div>
<blockquote
cite="mid:1438340555.5557.396.camel@wllt1771.nerc-wallingford.ac.uk"
type="cite">
<pre wrap="">Hi Marvin,
The mailing list server says you are not subscribed to the list. Maybe
you just signed up on a slightly different address, which is fine,
otherwise please check or you might not see all the replies.
Did you see my announcement on the list yesterday of QIIME 1.9.1?
Please try the updated version, but I don't think it will solve your
problem. My best guess is that you have some issue with your FASTA file
that is upsetting the parser.
To be sure, try running the filter with a small FASTA file like
/usr/local/bioinf/sampledata/nucleotide_seqs/multiple_seqs.fasta
This should definitely work.
Cheers,
TIM
On Fri, 2015-07-31 at 10:15 +0200, Marvin Djukic wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Dear Bio-Linux Users,
maybe you're able to help me with the following problem:
Anytime I try to use "filter_fasta.py" (qiime package) I get an error
message.
qiime > filter_fasta.py -f data.fas -o test -s
list
Traceback (most recent call last):
File "/usr/local/bin/filter_fasta.py", line 183, in <module>
main()
File "/usr/local/bin/filter_fasta.py", line 180, in main
negate)
File "/usr/local/bin/filter_fasta.py", line 84, in filter_fasta_fp
return filter_fasta(input_seqs,output_f,seqs_to_keep,negate)
File "/usr/lib/python2.7/dist-packages/qiime/filter.py", line 352,
in filter_fasta
for seq_id, seq in parse_fasta(input_seqs_f):
File
"/usr/lib/python2.7/dist-packages/skbio/parse/sequences/fasta.py",
line 136, in parse_fasta
for rec in finder(infile):
File
"/usr/lib/python2.7/dist-packages/skbio/parse/record_finder.py", line
150, in parser
line = constructor(l)
TypeError: descriptor 'strip' requires a 'str' object but received a
'tuple'
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).
Is there anyone who is able to help me with this issue?
Thanks a lot,
best regards,
Marvin
print_qiime_config_all:
System information
==================
Platform: linux2
Python version: 2.7.6 (default, Jun 22 2015, 17:58:13) [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:
<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>
Dependency 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:
<a class="moz-txt-link-freetext" href="http://qiime.org/install/qiime_config.html">http://qiime.org/install/qiime_config.html</a>
<a class="moz-txt-link-freetext" href="http://qiime.org/tutorials/parallel_qiime.html">http://qiime.org/tutorials/parallel_qiime.html</a>
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 0.027s
OK
Here are the versions of the packages that QIIME depends on as
reported by
the system package manager:
ampliconnoise : 1.29-2
blast2 : 1:2.2.26.20120620-7
bwa : 0.7.12-0biolinux1
cd-hit : 4.6.1-2012-08-27-2
chimeraslayer : 20101212+dfsg-1
clearcut : 1.0.9-0biolinux1.1
clustalw : 2.1+lgpl-4
ea-utils : 1.1.2+dfsg-1biolinux1
emperor : 0.9.51-0biolinux1
fasttree : 2.1.7-1biolinux1.1
infernal : 1.1.1-2ubuntu1
mafft : 7.215-0biolinux1
mothur : 1.34.4+repack-0biolinux1
muscle : 1:3.8.31-1
parsinsert : 1.04-1biolinux1.1
pynast : 1.2.2-0biolinux1.1
python : 2.7.5-5ubuntu3
python-biom-format : 2.1.4-0biolinux2
python-burrito : 0.9.0-0biolinux3
python-burrito-fillings : 0.1.0-0biolinux4
python-cogent : 1.5.3-2biolinux2
python-matplotlib : 1.3.1-1ubuntu5
python-mpi4py : 1.3.1+hg20131106-1build3
python-numpy : 1:1.8.2-0ubuntu0.1
python-pandas : 0.13.1-2ubuntu2
python-qcli : 0.1.0-1
python : 2.7.5-5ubuntu3
qiime-data : 1.9.0+dfsg-0biolinux5
qiime-default-reference : 0.1.1-0biolinux2
r-cran-optparse : 1.3.0-1cran1ppa0
raxml : 8.0.26-0biolinux1
rdp-classifier : 2.10.2+dfsg-0biolinux1
seqprep : 1.1-0biolinux2
sortmerna : 2.0-0biolinux1
sumatra : 1.0.01-0ubuntu1
swarm : 1.2.20-0biolinux1
vsearch : 1.1.1.nodata-0biolinux1
OK
--
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>
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<a class="moz-txt-link-freetext" href="http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux">http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux</a>
</pre>
</blockquote>
<pre wrap="">
</pre>
</blockquote>
<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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