[Bio-Linux] qiime filter_fasta.py problem
Tim Booth
tbooth at ceh.ac.uk
Fri Jul 31 07:02:35 EDT 2015
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
>
>
> --
> 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
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
--
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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