Cutadapt error

[Former user]

Hi,

I have a problem when trying to run miARma at the adapter cutting step. Here I enclose output from terminal:

CUTADAPT ERROR :: system args failed: 256 (mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/ ; cut_adapt -b TGGAATTCTCGGGTGCCAAGG -m 18 -M 40 -q 25 Examples/basic_examples/miRNAs/reads///5_ADXS_1_01.fastq.gz > Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/5_ADXS_1_01_cut.fastq 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.83498.log) at lib/CbBio/RNASeq/Adapt.pm line 856.

and log files

Thank You in advance, Adrian

[Eduardo Andres Leon]

Hi, Which Operative system + version are you using ?

Thanks in advance

[Adrian Kasztelan]

Hi, i am using macOS Mojave 10.14

[Eduardo Andres Leon]

Do you have the Xcode app installed ?

I'm also using Mojave and its correctly working:

eandres$ uname -a
Darwin PCBio1105118.ipb.csic.es 18.2.0 Darwin Kernel Version 18.2.0: Mon Nov 12 20:24:46 PST 2018; root:xnu-4903.231.4~2/RELEASE_X86_64 x86_64
eandres$ ~/bin/miARma/bin/Darwin/cutadapt/cut_adapt --version
1.3

[Adrian Kasztelan]

Yes, I have Xcode. Kernel and cut adapt version the same as yours.

I'm sorry to bother you, once my system perform update few minutes ago adapter trimming goes nicely.

Greetings, Adrian

[Eduardo Andres Leon]

Wow ....

and python ?:

eandres$ python --version Python 2.7.10

[Adrian Kasztelan]

python 2.7.13 but I am pretty sure that I have 3.6 also

[Eduardo Andres Leon]

Yes ... and I'm sure 3.6 (3.4 in my case) is the default. In my case 2.7 is the default:

yoda:RSeQC-2.6.4 eandres$ **python2.7** ~/bin/miARma/bin/Darwin/cutadapt/cut_adapt --version
1.3



yoda:RSeQC-2.6.4 eandres$ **python3.4** ~/bin/miARma/bin/Darwin/cutadapt/cut_adapt --version
Traceback (most recent call last):
  File "/Users/eandres/bin/miARma/bin/Darwin/cutadapt/cut_adapt", line 9, in <module>
    from cutadapt.scripts import cutadapt
  File "/Users/eandres/bin/miARma1.6.1/bin/Darwin/cutadapt/cutadapt/scripts/cutadapt.py", line 74, in <module>
    from cutadapt.adapters import Adapter, ColorspaceAdapter, BACK, FRONT, PREFIX, ANYWHERE
  File "/Users/eandres/bin/miARma1.6.1/bin/Darwin/cutadapt/cutadapt/adapters.py", line 4, in <module>
    from cutadapt import align, colorspace
  File "/Users/eandres/bin/miARma1.6.1/bin/Darwin/cutadapt/cutadapt/align.py", line 225, in <module>
    from cutadapt.calign import globalalign_locate
ImportError: dlopen(/Users/eandres/bin/miARma1.6.1/bin/Darwin/cutadapt/cutadapt/calign.so, 2): Symbol not found: _PyString_Type
  Referenced from: /Users/eandres/bin/miARma1.6.1/bin/Darwin/cutadapt/cutadapt/calign.so
  Expected in: flat namespace
 in /Users/eandres/bin/miARma1.6.1/bin/Darwin/cutadapt/cutadapt/calign.so

[Eduardo Andres Leon]

So, can you change the fist line in .... miARma/bin/Darwin/cutadapt/cut_adapt ?

Change this: "#!/usr/bin/env python"

for: "#!/usr/bin/python2.7"

I guess this should work

[Adrian Kasztelan]

ok done. thank you for your help

[Eduardo Andres Leon]

It was a pleasure