File not found error

[biocore]

File not found error

[ekopylova]

Hmm ... this looks like that multithreading error I was receiving in my original parallel PR. @amnona mentioned he wasn't seeing the error any longer with his version (now merged into master). From my experience, the trimmed reads were not being written to a file (when using multithreading) and the resulting empty file caused failures in downstream analyses. I would suggest looking at these lines and determine why nothing is being written out to file even though trimming appears to be working correctly.

[amnona]

Strange...
Didn't encounter the mutithreading error on local mac/barnacle/travis...
Anyway, can try to look at the log ("log.newmonkies.neg") file to see
exactly what's going on
Jamie - let me know when u have time. And thanks!!!!

On Thu, Aug 11, 2016 at 9:53 AM, Evguenia Kopylova <[email protected]

wrote:

Hmm ... this looks like that multithreading error I was receiving in my
original parallel PR #33. @amnona
https://github.com/amnona mentioned he wasn't seeing the error any
longer with his version (now merged into master). From my experience, the
trimmed reads were not being written to a file (when using multithreading)
and the resulting empty file caused failures in downstream analyses. I
would suggest looking at these lines
https://github.com/biocore/deblur/blob/master/deblur/workflow.py#L561
and determine why nothing is being written out to file even though trimming
appears to be working correctly.

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
#39 (comment), or mute
the thread
https://github.com/notifications/unsubscribe-auth/AFkA8qUykgriLAPgwF766_xAZsCTfX6Mks5qesbmgaJpZM4JhJN_
.

[josenavas]

This error shows up when there is a missing dependency. Burrito-fillings was providing a useful error while the current implementation does not...

[amnona]

Aha!
seems like the problem is that the trim length (-t) is 150bp, whereas the
sequence length is only 100?
(guess we need to add a warning if the trim length is longer than the vast
majority of the sequences :) )
Does this make sense? can you rerun it with -t 100 ?

On Thu, Aug 11, 2016 at 10:48 PM, Jose Navas [email protected]
wrote:

This error shows up when there is a missing dependency. Burrito-fillings
was providing a useful error while the current implementation does not...

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
#39 (comment), or mute
the thread
https://github.com/notifications/unsubscribe-auth/AFkA8s30I5qG0fH2WZtr_A1g6RyTtYf-ks5qe3ySgaJpZM4JhJN_
.

[wasade]

@mortonjt, were you able to verify the trim length as the issue here?

[mortonjt]

This was a result of some dependency issues from not installing sortmerna or vsearch.