python permission denied problem & any way to avoid installing bowtie2

[yunli...@gmail.com]

Hi all,

I hava some questions when using kneaddata. I only need to use bmtagger to remove human reads. However, even I set --bmtagger parameter when running the program, the software will automatically check the installation of bowtie2 and indexing reference database bowtie2 used. Is there any way I can avoid installing bowtie2 and the related reference database if I only interested in bmtagger?

After I installed bowtie2 and finally can run the program, I have a “python permission denied problem”. I saw in the user manual "If you do not have write permissions to '/usr/lib/', then add the option "--user" to the install command." However, I already have python installed before I installed kneaddata. How can I solve the problem?

Here is the error:

Traceback (most recent call last):

  File "/usr/local/bin/kneaddata", line 9, in <module>

    load_entry_point('kneaddata==0.4.6.1', 'console_scripts', 'kneaddata')()

  File "/usr/local/lib/python2.7/dist-packages/kneaddata-0.4.6.1-py2.7.egg/kneaddata/knead_data.py", line 390, in main

    storageheavy.storage_heavy(args)

  File "/usr/local/lib/python2.7/dist-packages/kneaddata-0.4.6.1-py2.7.egg/kneaddata/storageheavy.py", line 888, in storage_heavy

    debug          = debug)

  File "/usr/local/lib/python2.7/dist-packages/kneaddata-0.4.6.1-py2.7.egg/kneaddata/storageheavy.py", line 280, in tag

    stdout=subprocess.PIPE)

  File "/usr/lib/python2.7/subprocess.py", line 679, in __init__

    errread, errwrite)

  File "/usr/lib/python2.7/subprocess.py", line 1249, in _execute_child

    raise child_exception

OSError: [Errno 13] Permission denied

Thanks,

Yun

[Andy Shi]

Hi Yun,

Thank you for your interest in KneadData! Unfortunately, because Bowtie2 is the default, its dependency gets checked every time. It's possible to not install bowtie2 by using the --bypass-dependencies flag when installing, e.g. you would use 

python setup.py install --bypass-dependencies

You may need to use sudo, or you may need to also include the --user flag. During installation, the reference databases for Bowtie2 are not downloaded.

The error you're getting probably means that KneadData can't execute the BMTagger executable. To check, do 

ls -l [PATH_TO_BMTAGGER]

and see if the first letters are "-rwx" or something similar. If it's not, you'll need to make BMTagger executable using

chmod u+x [PATH_TO_BMTAGGER]

Let me know if this helps. 

Thanks!

[yunli...@gmail.com]

Hi Andy,

Thank you for your email.

The BMTagger is executable, I can run it independently and I added the path in the command when I run kneaddata. If I tried to run in super user mode "sudo kneaddata ...." I get the following error, The "ImportError" will also appeared if I install the software by adding ''--user". Do you know what is wrong?

Traceback (most recent call last):

  File "/usr/local/bin/kneaddata", line 9, in <module>

    load_entry_point('kneaddata==0.4.6.1', 'console_scripts', 'kneaddata')()

  File "/usr/local/lib/python2.7/dist-packages/setuptools-12.2-py2.7.egg/pkg_resources/__init__.py", line 521, in load_entry_point

    return get_distribution(dist).load_entry_point(group, name)

  File "/usr/local/lib/python2.7/dist-packages/setuptools-12.2-py2.7.egg/pkg_resources/__init__.py", line 2631, in load_entry_point

    raise ImportError("Entry point %r not found" % ((group, name),))

ImportError: Entry point ('console_scripts', 'kneaddata') not found

Thanks,

Yun

[Andy Shi]

Hi Yun,

Can you post the command(s) you used to install kneaddata, and the commands you used to run kneaddata? It seems like kneaddata was not properly installed/configured.

[Yun Li]

Hi Andy,

For install I use: 

sudo python setup.py install

To run the program, if I use 

kneaddata --input test1.fastq --input2 test2.fastq --reference-db /home/qiime/BiosoftwareLibrary/hs38_ref/hs38 --bmtagger --output-prefix kneaddata_test --output kneaddata_output --extract --bmtagger-path /home/qiime/BiosoftwareLibrary/bmtools/bmtagger

2015-12-21 10:19:34,166 INFO: Initial number of reads: test1.fastq: 250

test2.fastq: 250

2015-12-21 10:19:34,167 INFO: Trimming...

2015-12-21 10:19:35,570 INFO: Finished running Trimmomatic. Checking output files exist... 

2015-12-21 10:19:35,579 INFO: Number of reads after trimming: /home/qiime/Desktop/TMP/kneaddata_output/kneaddata_test.trimmed.1.fastq: 200

/home/qiime/Desktop/TMP/kneaddata_output/kneaddata_test.trimmed.2.fastq: 200

/home/qiime/Desktop/TMP/kneaddata_output/kneaddata_test.trimmed.single.1.fastq: 8

/home/qiime/Desktop/TMP/kneaddata_output/kneaddata_test.trimmed.single.2.fastq: 37

2015-12-21 10:19:35,580 INFO: Decontaminating

Traceback (most recent call last):

  File "/usr/local/bin/kneaddata", line 9, in <module>

    load_entry_point('kneaddata==0.4.6.1', 'console_scripts', 'kneaddata')()

  File "/usr/local/lib/python2.7/dist-packages/kneaddata-0.4.6.1-py2.7.egg/kneaddata/knead_data.py", line 390, in main

    storageheavy.storage_heavy(args)

  File "/usr/local/lib/python2.7/dist-packages/kneaddata-0.4.6.1-py2.7.egg/kneaddata/storageheavy.py", line 888, in storage_heavy

    debug          = debug)

  File "/usr/local/lib/python2.7/dist-packages/kneaddata-0.4.6.1-py2.7.egg/kneaddata/storageheavy.py", line 280, in tag

    stdout=subprocess.PIPE)

  File "/usr/lib/python2.7/subprocess.py", line 679, in __init__

    errread, errwrite)

  File "/usr/lib/python2.7/subprocess.py", line 1249, in _execute_child

    raise child_exception

OSError: [Errno 13] Permission denied

If I run with superuser mode:

sudo kneaddata --input test1.fastq --input2 test2.fastq --reference-db /home/qiime/BiosoftwareLibrary/hs38_ref/hs38 --bmtagger --output-prefix kneaddata_test --output kneaddata_output --extract --bmtagger-path /home/qiime/BiosoftwareLibrary/bmtools/bmtagger

Traceback (most recent call last):

  File "/usr/local/bin/kneaddata", line 9, in <module>

    load_entry_point('kneaddata==0.4.6.1', 'console_scripts', 'kneaddata')()

  File "/usr/local/lib/python2.7/dist-packages/setuptools-12.2-py2.7.egg/pkg_resources/__init__.py", line 521, in load_entry_point

    return get_distribution(dist).load_entry_point(group, name)

  File "/usr/local/lib/python2.7/dist-packages/setuptools-12.2-py2.7.egg/pkg_resources/__init__.py", line 2631, in load_entry_point

    raise ImportError("Entry point %r not found" % ((group, name),))

ImportError: Entry point ('console_scripts', 'kneaddata') not found

Thank you so much,

Yun

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[Andy Shi]

Hi Yun,

I think that the bmtagger-path option is specified incorrectly. It seems like you set it to the folder that contains the bmtagger executable, but not to the bmtagger executable itself. If you use the first command as

kneaddata --input test1.fastq --input2 test2.fastq --reference-db /home/qiime/BiosoftwareLibrary/hs38_ref/hs38 --bmtagger --output-prefix kneaddata_test --output kneaddata_output --extract --bmtagger-path /home/qiime/BiosoftwareLibrary/bmtools/bmtagger/bmtagger.sh

it might fix your issue.

[yunli...@gmail.com]

Hi Andy,

I tried. I still got permisson denied error. I tried to use bowtie2, and I do not have any problem in running kneaddata. However, if I use bmtagger, I will have python permisson issue.

Thanks,

Yun