[Bio-Linux] qiime filter_fasta.py problem
Marvin Djukic
mdjukic1 at gwdg.de
Fri Jul 31 04:15:01 EDT 2015
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:
https://github.com/biocore/qiime-default-reference/releases/tag/0.1.1
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:
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 0.027s
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: mdjukic1 at gwdg.de
http://appmibio.uni-goettingen.de
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