[Bio-Linux] qiime filter_fasta.py problem
Tim Booth
tbooth at ceh.ac.uk
Fri Jul 31 08:21:36 EDT 2015
Hi Marvin,
OK, just had a second look at your error and it says:
... "/usr/local/bin/filter_fasta.py" ...
This is not part of the QIIME package. The program should be:
/usr/lib/qiime/bin/filter_fasta.py
So it looks like you have some rogue QIIME scripts on your system.
Possibly at some point you tried to install QIIME using the "pip
install ..." mechanism?
Please try removing /usr/local/bin/filter_fasta.py. In fact, unless you
know you have explicitly installed Python scripts into /usr/local/bin it
is safe to get rid of them all:
sudo rm /usr/local/bin/*.py
Does that fix it?
Cheers,
TIM
> I updated Qiime to 1.9.1, but the error is still exactly the same. I'm
> also not able to run filter_fasta.py with the sample data set. Same
> error.
> Maybe someone else has an idea. Don't know what to change/do at the
> moment.
>
> Thanks a lot,
> regards,
> Marvin
>
>
> On 31.07.2015 13:02, Tim Booth wrote:
>
> > 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:
> > > 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
> > >
> > >
> >
--
Tim Booth <tbooth at ceh.ac.uk>
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
http://environmentalomics.org/bio-linux
+44 1491 69 2297
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