Binsanity-wf fails

[donovan-h-parks]

Hello,

I am trying to run the "Binsanity-wf" command as follows: Binsanity-wf -f <my_assembly_dir> -l <my_assembly> -c binsanity.profile.cov.x100.lognorm -o output --threads 20

This successfully runs the Binsanity and CheckM, but then immediately fails after CheckM:

*******************************************************************************
 [CheckM - qa] Tabulating genome statistics.
*******************************************************************************

  Calculating AAI between multi-copy marker genes.

  Reading HMM info from file.
  Parsing HMM hits to marker genes:
    Finished parsing hits for 10 of 10 (100.00%) bins.

  { Current stage: 0:00:06.542 || Total: 0:06:01.380 }
Traceback (most recent call last):
  File "/gnu/store/vzmhc8h9i20as615l0lmbnjqb3lww85s-binsanity-0.2.5.5/bin/..Binsanity-wf-real-real", line 429, in <module>
    shutil.copyfileobj(readfile,outfile)
  File "/srv/sw/python/2.7.4/lib/python2.7/shutil.py", line 52, in copyfileobj
    fdst.write(buf)
ValueError: I/O operation on closed file

Do you have any insights into what might be causing this issue?

[edgraham]

Hi Donovan,

Can you send me the version of BinSanity you are running?

Regards, Elaina Graham

On Mon, May 29, 2017 at 2:32 PM, Donovan Parks notifications@github.com wrote:

Hello,

I am trying to run the "Binsanity-wf" command as follows: Binsanity-wf -f -l -c binsanity.profile.cov.x100.lognorm -o output --threads 20

This successfully runs the Binsanity and CheckM, but then immediately fails after CheckM:

---

[CheckM - qa] Tabulating genome statistics.

---

Calculating AAI between multi-copy marker genes.

Reading HMM info from file. Parsing HMM hits to marker genes: Finished parsing hits for 10 of 10 (100.00%) bins.

{ Current stage: 0:00:06.542 || Total: 0:06:01.380 } Traceback (most recent call last): File "/gnu/store/vzmhc8h9i20as615l0lmbnjqb3lww85s-binsanity-0.2.5.5/bin/..Binsanity-wf-real-real", line 429, in shutil.copyfileobj(readfile,outfile) File "/srv/sw/python/2.7.4/lib/python2.7/shutil.py", line 52, in copyfileobj fdst.write(buf) ValueError: I/O operation on closed file

Do you have any insights into what might be causing this issue?

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[donovan-h-parks]

I'm running v0.2.5.5.

[edgraham]

Hi Donovan,

Thanks for the information. Try updating the version to v0.2.5.9. I think this may be an issue that occured when I was updating versions between v0.2.5.4 and v0.2.5.5 where I accidently closed a file I was writing to in python before BinSanity was finished using it. I fixed it in the subsequent versions.

If that doesn't solve it please let me know!

Regards, Elaina

On Mon, May 29, 2017 at 5:20 PM, Donovan Parks notifications@github.com wrote:

I'm running v0.2.5.5.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/edgraham/BinSanity/issues/13#issuecomment-304747309, or mute the thread https://github.com/notifications/unsubscribe-auth/AQXxo5MvkpWcIdmpH3URKfJ8XykVi6Cxks5r-2DcgaJpZM4Nppfp .

[donovan-h-parks]

Yep, that solved the issue. Thanks.