error after running recycle.py

[OAF12]

recycle.py -g assembly_graph.fastg -k 55 -b reads_pe_primary.sort.bam I got the below erro Traceback (most recent call last): File "/home/omnah486/miniconda2/bin/recycle.py", line 4, in import('pkg_resources').run_script('recycler==0.6', 'recycle.py') File "/home/omnah486/miniconda2/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/init.py", line 744, in run_script File "/home/omnah486/miniconda2/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/init.py", line 1506, in run_script File "/home/omnah486/miniconda2/lib/python2.7/site-packages/recycler-0.6-py2.7.egg/EGG-INFO/scripts/recycle.py", line 62, in

AttributeError: 'module' object has no attribute 'AlignmentFile'

[rozovr]

This looks like a pysam related error. Please check pysam is installed properly.

[OAF12]

Thanks for your reply, I re-installed pysam. Now I got that below error:

Traceback (most recent call last): File "/home/omnah486/miniconda2/bin/recycle.py", line 4, in import('pkg_resources').run_script('recycler==0.6', 'recycle.py') File "/home/omnah486/miniconda2/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/init.py", line 744, in run_script File "/home/omnah486/miniconda2/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/init.py", line 1506, in run_script File "/home/omnah486/miniconda2/lib/python2.7/site-packages/recycler-0.6-py2.7.egg/EGG-INFO/scripts/recycle.py", line 69, in

NameError: name 'get_fastg_digraph' is not defined

[sergiomorgado]

The same error here: NameError: name 'get_fastg_digraph' is not defined

All dependencies are ok.

[rozovr]

Can you please me how you installed recycler? I.e., did you do git pull, download a zip, etc. and where from? That will help me diagnose why this happens.

[OAF12]

Hi,

I did non-bioconda install steps, following the instructions in https://github.com/Shamir-Lab/Recycler?

Best regards

Omneya

---

From: Roye Rozov notifications@github.com Sent: Saturday, September 2, 2017 09:24 To: Shamir-Lab/Recycler Cc: Omneya Ahmed Abdel Hafez Sayed Osman; Author Subject: Re: [Shamir-Lab/Recycler] error after running recycle.py (#14)

Can you please me how you installed recycler? I.e., did you do git pull, download a zip, etc. and where from? That will help me diagnose why this happens.

- You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Shamir-Lab/Recycler/issues/14#issuecomment-326728011, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AXrXptZIEeaust7y7L0TLd5Qb_q_dvR0ks5seQLBgaJpZM4OvgZW.

[sergiomorgado]

I installed using conda.

[OAF12]

I found that some persons had a problem with recycler installed by bioconda then I installed non-bioconda and I did both.

https://github.com/Shamir-Lab/Recycler/issues/9

But still the final command is not working

Best

Omneya

---

From: sergiomorgado notifications@github.com Sent: Saturday, September 2, 2017 21:13 To: Shamir-Lab/Recycler Cc: Omneya Ahmed Abdel Hafez Sayed Osman; Author Subject: Re: [Shamir-Lab/Recycler] error after running recycle.py (#14)

I installed using conda.

- You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Shamir-Lab/Recycler/issues/14#issuecomment-326764055, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AXrXpiBeHCwntA06Pjxj1ltC7IUL657Pks5seajPgaJpZM4OvgZW.

[rozovr]

@OAF12 and @sergiomorgado , sorry for my delay, am wrapping up my thesis now; will look into this soon