[captainentropy]

I see. Yes, that makes sense now. My match is at the beginning of the read so there's nothing to the left of it (and thus empty).

Thanks!

[mmartin]

Hi, cutadapt 1.6 is now available. Here's a copy of the changelog.

There are no new features, but some bugs have been fixed and the documentation is now available at https://cutadapt.readthedocs.org/ and has been updated quite a bit.

• Fix issue 77: Ensure --format=... can be used even with paired-end input.
• Fix issue 79: Sometimes output files would be incomplete because they were not closed correctly.
• Extensive work on the documentation. It's now available at https://cutadapt.readthedocs.org/.
• The alignment algorithm is a tiny bit faster.
• For 3' adapters, statistics about the bases preceding the trimmed adapter are collected and printed. If one of the bases is overrepresented, a warning is shown since this points to an incomplete adapter sequence. This happens, for example, when a TruSeq? adapter is used but the A overhang is not taken into account when running cutadapt.
• Duo to code cleanup, there is a change in behavior: If you use --discard-trimmed or --discard-untrimmed in combination with --too-short-output or --too-long-output, then cutadapt now writes also the discarded reads to the output files given by the --too-short or --too-long options. If anyone complains, I will consider reverting this.
• Galaxy support files are now in a separate repository at https://bitbucket.org/lance_parsons/...galaxy_wrapper . Thanks to Lance Parsons for his work on this.

[Francy87]

epicentre scriptseq v2 adaptors trimming

Hi all!
I want to use cuadapt to trim adaptors from my single end reads. The libraries were generated by using the scriptseq v2 kit by epicentre. The kit protocol report some adaptor sequences and the indexed primers, but I'm not sure about which of them I should look for (attached the kit protocol - adaptors sequences at page 11 - and the indexed primers used (1 to 12))

Anyone can help me?

Thanks a lot
Francesca

[pbest]

The kit protocol report some adaptor sequences and the indexed primers, but I'm not sure about which of them I should look for

Hi Francy,

for single end reads you would normally only expect contamination with Adapter-Sequences at the 3'-ends of your reads. I haven't read the protocol you attached in detail - but to my knowledge this is the information you want:

The sequence of each ScriptSeq Index PCR Primer is:
5′ CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT 3′

Use the reverse-complement of the above sequence with cutadapts -a option. You can even keep the N's in the sequence - cutadapt knows how to handle them.
So try cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG

and then have a look at the report - if there is a reasonable number of reads trimmed it should be correct.

Cheers Phil

[mmartin]

Hi Francy,

I think Phil gave the correct answer. It seems the adapter sequence is compatible with Illumina’s adapter (it probably has to be for it to work), and so you need to trim the same adapter sequence.

If you want to shorten the command a bit, it is probably enough to use only the first 13 or so bases of the full adapter sequence: -a AGATCGGAAGAGC. That makes cutadapt also slightly faster.

Marcel

[mmartin]

Cutadapt 1.7 released

Hi there, cutadapt 1.7 is now available. Here are the most important new features:

• Support for IUPAC characters
• Demultiplexing of FASTQ files
• Added an "anchored 3' adapter" type

And of course there are some bugfixes and closed issues. See also the full changelog. If you want know about future cutadapt releases, you can also follow me on Twitter.

The next release will add proper paired-end trimming support. That is, you can then trim both reads at the same time without running cutadapt twice. Check out the 'paired' branch on Github if you are interested.

Update: If you get the message "OSError: [Errno 2] No such file or directory: 'cutadapt/_align.pyx'", then please update to cutadapt 1.7.1, which fixes the error.

[pbest]

Hi Marcel,

danke für den IUPAC-Support.
Das ist ziemlich nützlich für RRBS-Daten um die aufgeüllten CGs los zu werden.

MFG Phil

[mmartin]

danke für den IUPAC-Support.
Das ist ziemlich nützlich für RRBS-Daten um die aufgeüllten CGs los zu werden.

Sure! IUPAC support has been on my list for a while, was good to have this finally implemented.

[sidsv]

Hello!

I have a problem using cutadapt 1.7.1. I downloaded it from

https://pypi.python.org/packages/source/c/cutadapt/cutadapt-1.7.1.tar.gz

untared, went inside the cutadapt-1.7.1 directory and ran

python setup.py install --user

to install it localy. But when a ran

/home/<myusername>/.local/bin/cutadapt --version

it showed 1.2.1 version. And there was no -u/--cut option that I need in order to cut last 15 bases. Maybe I do something wrong with it?

Any help is appreciated!

[mmartin]

Which output did

python setup.py install --user

produce? Were there any error messages?

[sidsv]

Thank you for quick reply!

I looked through the output and saw no error or warning messages.

I removed cutadapt-1.7.1 directory and /home/<username>/.local/bin/cutadapt and reinstalled it with the same command.

Complete output is:

running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/cutadapt
copying cutadapt/seqio.py -> build/lib.linux-x86_64-2.7/cutadapt
copying cutadapt/compat.py -> build/lib.linux-x86_64-2.7/cutadapt
copying cutadapt/xopen.py -> build/lib.linux-x86_64-2.7/cutadapt
copying cutadapt/qualtrim.py -> build/lib.linux-x86_64-2.7/cutadapt
copying cutadapt/adapters.py -> build/lib.linux-x86_64-2.7/cutadapt
copying cutadapt/align.py -> build/lib.linux-x86_64-2.7/cutadapt
copying cutadapt/modifiers.py -> build/lib.linux-x86_64-2.7/cutadapt
copying cutadapt/report.py -> build/lib.linux-x86_64-2.7/cutadapt
copying cutadapt/colorspace.py -> build/lib.linux-x86_64-2.7/cutadapt
copying cutadapt/__init__.py -> build/lib.linux-x86_64-2.7/cutadapt
creating build/lib.linux-x86_64-2.7/cutadapt/scripts
copying cutadapt/scripts/cutadapt.py -> build/lib.linux-x86_64-2.7/cutadapt/scripts
copying cutadapt/scripts/__init__.py -> build/lib.linux-x86_64-2.7/cutadapt/scripts
running build_ext
building 'cutadapt._align' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/cutadapt
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/python2.7 -c cutadapt/_align.c -o build/temp.linux-x86_64-2.7/cutadapt/_align.o
gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-x86_64-2.7/cutadapt/_align.o -o build/lib.linux-x86_64-2.7/cutadapt/_align.so
building 'cutadapt._qualtrim' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/python2.7 -c cutadapt/_qualtrim.c -o build/temp.linux-x86_64-2.7/cutadapt/_qualtrim.o
gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-x86_64-2.7/cutadapt/_qualtrim.o -o build/lib.linux-x86_64-2.7/cutadapt/_qualtrim.so
building 'cutadapt._seqio' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/python2.7 -c cutadapt/_seqio.c -o build/temp.linux-x86_64-2.7/cutadapt/_seqio.o
gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-x86_64-2.7/cutadapt/_seqio.o -o build/lib.linux-x86_64-2.7/cutadapt/_seqio.so
running build_scripts
creating build/scripts-2.7
copying and adjusting bin/cutadapt -> build/scripts-2.7
changing mode of build/scripts-2.7/cutadapt from 664 to 775
running install_lib
copying build/lib.linux-x86_64-2.7/cutadapt/_seqio.so -> /home/<username>/.local/lib/python2.7/site-packages/cutadapt
copying build/lib.linux-x86_64-2.7/cutadapt/_qualtrim.so -> /home/<username>/.local/lib/python2.7/site-packages/cutadapt
copying build/lib.linux-x86_64-2.7/cutadapt/_align.so -> /home/<username>/.local/lib/python2.7/site-packages/cutadapt
running install_scripts
copying build/scripts-2.7/cutadapt -> /home/<username>/.local/bin
changing mode of /home/<username>/.local/bin/cutadapt to 775
running install_egg_info
Removing /home/<username>/.local/lib/python2.7/site-packages/cutadapt-1.7.1.egg-info
Writing /home/<username>/.local/lib/python2.7/site-packages/cutadapt-1.7.1.egg-info

Then I tried

/home/<username>/.local/bin/cutadapt --version

and got "1.2.1".

[sidsv]

I managed to install cutadapt 1.7.1 on my notebook locally (into /home/<username>/.local/bin) without a problem. All I described above I did on our server where cutadapt 1.2.1 is already installed 'globally' (in /usr/local/bin). My friend supposed that maybe when I launch setup.py in my cutadapt-1.7.1 directory it finds other cutadapt sources (which are 1.2.1) and installs them into my /home/<username>/.local/bin directory. So I constantly have 1.2.1 version. Maybe he is right, because when I try to install cutadapt locally using pip with a command

 pip install --user cutadapt

pip says that

Requirement already satisfied (use --upgrade to upgrade): cutadapt in /usr/local/lib/python2.7/dist-packages
Cleaning up...

[mmartin]

Very strange ... I think your friend is on the right track, but I’m guessing the problem is slightly different: The bin/cutadapt binary is actually just a small wrapper that loads the actual package and starts it. It could be that it picks up the wrong (old) package in your case. To confirm, can you please post the output of the following commands:

head -n 1 $HOME/.local/bin/cutadapt
python -c 'import sys; print sys.path'
python -c 'import cutadapt; print cutadapt.__file__'

Also, you could try running

pip install --user cutadapt==1.7.1

Then pip should actually install the version you requested instead of telling you the software is already installed.

[sidsv]

Martin, thanks!

First three commands:

>$ head -n 1 $HOME/.local/bin/cutadapt
#!/usr/bin/python

>$ python -c 'import sys; print sys.path'
['', '/usr/local/lib/python2.7/dist-packages/screed-0.7-py2.7.egg', '/usr/local/lib/python2.7/dist-packages/pbcore-0.8.0-py2.7.egg', '/usr/local/lib/python2.7/dist-packages', '/usr/local/lib/python2.7/dist-packages/distribute-0.6.34-py2.7.egg', '/usr/local/lib/python2.7/dist-packages/ete2-2.2rev1056-py2.7.egg', '/usr/local/lib/python2.7/dist-packages/pbtools.pbdagcon-0.2.3-py2.7-linux-x86_64.egg', '/usr/local/lib/python2.7/dist-packages/MAVR-1.0-py2.7.egg', '/usr/lib/python2.7', '/usr/lib/python2.7/plat-linux2', '/usr/lib/python2.7/lib-tk', '/usr/lib/python2.7/lib-old', '/usr/lib/python2.7/lib-dynload', '/home/<username>/.local/lib/python2.7/site-packages', '/usr/local/lib/python2.7/dist-packages', '/usr/lib/python2.7/dist-packages', '/usr/lib/python2.7/dist-packages/PIL', '/usr/lib/python2.7/dist-packages/gtk-2.0', '/usr/lib/pymodules/python2.7']

>$ python -c 'import cutadapt; print cutadapt.__file__'
cutadapt/__init__.pyc

And I tried to install cutadapt 1.7.1 with pip, but it says that cutadapt 1.2.1 is already installed, tries to remove its files and fails:

>$ pip install --user cutadapt==1.7.1
Downloading/unpacking cutadapt==1.7.1
  Downloading cutadapt-1.7.1.tar.gz (451Kb): 451Kb downloaded
  Running setup.py egg_info for package cutadapt
    
Installing collected packages: cutadapt
  Found existing installation: cutadapt 1.2.1
    Uninstalling cutadapt:
Exception:
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/pip/basecommand.py", line 126, in main
    self.run(options, args)
  File "/usr/lib/python2.7/dist-packages/pip/commands/install.py", line 228, in run
    requirement_set.install(install_options, global_options)
  File "/usr/lib/python2.7/dist-packages/pip/req.py", line 1089, in install
    requirement.uninstall(auto_confirm=True)
  File "/usr/lib/python2.7/dist-packages/pip/req.py", line 476, in uninstall
    paths_to_remove.remove(auto_confirm)
  File "/usr/lib/python2.7/dist-packages/pip/req.py", line 1391, in remove
    renames(path, new_path)
  File "/usr/lib/python2.7/dist-packages/pip/util.py", line 248, in renames
    shutil.move(old, new)
  File "/usr/lib/python2.7/shutil.py", line 300, in move
    os.unlink(src)
OSError: [Errno 13] Permission denied: '/usr/local/lib/python2.7/dist-packages/cutadapt-1.2.1.egg-info'

Storing complete log in /home/<username>/.pip/pip.log

[mmartin]

I made a mistake, could you please change into some other directory before you run the third command, like so:

cd /; python -c 'import cutadapt; print cutadapt.__file__'

And I tried to install cutadapt 1.7.1 with pip, but it says that cutadapt 1.2.1 is already installed, tries to remove its files and fails:

I don’t have an explanation for that, and I could not reproduce it: I installed an old version of cutadapt into /usr/local (as root) and then tried the pip install --user command that I gave you and it did not even try to remove the old version. Which distribution are you on and what does

pip --version

say?