[Bio-Linux] qiime filter_fasta.py problem
Marvin Djukic
mdjukic1 at gwdg.de
Fri Jul 31 07:39:12 EDT 2015
Hi Tim,
thanks for your reply. (Now I should be subscribed to the list.)
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
>>
>>
>> --
>> 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
--
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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