[Bio-Linux] qiime filter_fasta.py problem
Marvin Djukic
mdjukic1 at gwdg.de
Fri Jul 31 08:26:06 EDT 2015
Hi Tim,
You're right - I guess I manually installed it the wrong way and didn't
delete all "old" files.
And yes, that fixed it. MANY many thanks.
Regards,
Marvin
On 31.07.2015 14:21, Tim Booth wrote:
> 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
>>>>
>>>>
--
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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