Error with bundled cut_adapt on CentOS

[Guillermo Marco Puche]

Hello Eduardo,

I've managed to run miARma from start to end without any issue from start to end on my local Ubuntu desktop. However I'm having some trouble running miARma on my computing CentOS cluster environment.

The miRNA pipeline stops when cutadapt runs:

/share/apps/local/miarma/bin/Linux/cutadapt/cut_adapt  --help
Traceback (most recent call last):
  File "/share/apps/local/miarma/bin/Linux/cutadapt/cut_adapt", line 9, in <module>
    from cutadapt.scripts import cutadapt
  File "/share/apps/local/miarma/bin/Linux/cutadapt/cutadapt/scripts/cutadapt.py", line 74, in <module>
    from cutadapt.adapters import Adapter, ColorspaceAdapter, BACK, FRONT, PREFIX, ANYWHERE
  File "/share/apps/local/miarma/bin/Linux/cutadapt/cutadapt/adapters.py", line 4, in <module>
    from cutadapt import align, colorspace
  File "/share/apps/local/miarma/bin/Linux/cutadapt/cutadapt/align.py", line 225, in <module>
    from cutadapt.calign import globalalign_locate
ImportError: /share/apps/local/miarma/bin/Linux/cutadapt/cutadapt/calign.so: undefined symbol: PyUnicodeUCS4_DecodeUTF8

From what I've read this may be due to the environment used to build the library. I've tried to re-build the cutadapt library included in miARma package without success. At this moment I cannot recompile python interpreter on this env with the following flags.

--enable-unicode=ucs4

So I think the easiest is to try to build cutadapt with my current Python env. Could you please tell me how did you build cutadapt inside miARma.

Regards,

[Eduardo Andres Leon]

Hi, In fact, you don't need to install cutadapt inside miARma. miARma first uses the software in the path, if there is no cut_adapt in the path, then it uses its own. So, my recommendation is to download cutadapt 1.3 (this is important as we have different issues with other versions) and install it wherever you want and export it in the path. If the installation is correct (try with a fastq file to test it), miARma will use it

By the way, which CentOs version are you using? E

[Guillermo Marco Puche]

Hello Eduardo,

Indeed it's an old CentOS version: CentOS release 6.6 Regarding to cutadapt, miARma runs a "cut_adapt" python script that uses cutadapt library. From my experience, I've always run cutadapt with the command "cutadapt" of the binary installed from pip install cutadapt

I'm trying to build the cutadapt 1.13 version but I can't manage to get the same files stored inside cutadapt from miARma installation. As I can see miARma executes the command "cut_adapt" and not cutadapt. I don't get how to get this "cut_adapt" script. I've tried compiling with both:

python setup.py build
python setup.py install --user

[Eduardo Andres Leon]

Have you tried to make an alias: ln -s cutadapt cut_adapt ? (I'm not sure why the binary in miARma is called cut_adapt instead of cutadapt)

[Guillermo Marco Puche]

I'm having troubles compiling cutadapt on my cluster. I'll try linking cutadapt binary from pip install and report asap.

[Guillermo Marco Puche]

Hello Eduardo, I'm unable to compile from source but I've installed cutadapt 1.16 through pip. Will this version work with miRNA pipeline?

[Eduardo Andres Leon]

Hi , I'm not really sure, I've tested from 1.0 to 1.3 and all of them worked correctly.

Don't forget to create a link from cutadapt binary to cut_adapt (the one needed in miARma).

[Guillermo Marco Puche]

Hello Eduardo, I'm currently testing with a symbolic link to cutadapt 1.16 and it seems to be working fine. I've read cutadapt changelog and mainly all the releases post 1.13 have been bug fixes, so I think it should work.

[Eduardo Andres Leon]

That's a fantastic news!

Did you now if this new version is threaded ?

[Guillermo Marco Puche]

Indeed it is for version 1.15+. I can't test it since parallel processing only works on Python 3 and I don't have it set on my computing environment. If you want to check changelog: https://cutadapt.readthedocs.io/en/stable/changes.html

[Guillermo Marco Puche]

Resolved linking cut_adapt binary from miARma to cutadapt 1.6 installed on system.