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**GenoMax** · 07-02-2014, 11:08 AM

A mere possibility, but have you looked to see if there are any non-printable/control character differences between the two whitelist files?

**OstanNick** · 07-02-2014, 11:15 AM

Hey Genomax,

I'm pretty sure both files are identical from a character point of view -- I used the same script to generate all of the files except I just hard code in my run name (mxxxx_xxxx_xxxxxxxxx).

The only difference between the way I generated my original (working) whitelist and my 7 new (non-working white lists) was that:

In my original, I copy/pasted all of the printed lines directly from the terminal, into a new 'whitelist.txt' file.

In the new ones, I used the output [(script) > whitelist.txt] argument. So I just re-generated one of my new whitelists and copy/pasted instead. I'll let you know if it works once the current job in queue is finished.

**OstanNick** · 07-02-2014, 11:23 AM

Wow,

For some reason, outputting it to a .txt file via the '>' when I ran my script caused it to mess up.

Copy+paste directly from the terminal seemed to do the trick...

Why would that ever occur?

**GenoMax** · 07-02-2014, 11:34 AM

Did you move the whitelist file between two OS's (e.g. OS X to Unix)?

**OstanNick** · 07-02-2014, 11:35 AM

No sir, everything has stayed on my Ubuntu OS (12.04)

**GenoMax** · 07-02-2014, 11:43 AM

So in what way was the file different between the copy/paste and script methods (e.g. http://alvinalexander.com/blog/post/...s-in-text-file)

**OstanNick** · 07-02-2014, 11:59 AM

Neither of them had any non-ASCII characters

**rhall** · 07-03-2014, 08:17 AM

Glad you got it working, my guess from the error

Code:

Invalid whitelist format for ''

a blank line at the end of the file? Looking at the code, the line being read that is invalid is returned between the quotes:

Code:

 emsg = "Invalid whitelist format for '{s}' in file {f}.".format(s=line.strip(), f=self._whitelist_file)

**OstanNick** · 07-03-2014, 08:36 AM

I just checked all of them that I generated using the >output and none of them have a blank line anywhere. Very strange. However, I don't want to take up your time trying to solve something that's practically already fixed. I just generated all of mine manually via copy/paste.

Thanks,
Nick

**rhall** · 07-03-2014, 08:48 AM

It's not time wasted if we can find and fix a bug

If you want to attach examples of the text files that work and do not work (hopefully they won't get reformatted in the attachment) I can take a look at what is happening. Alternatively I can give you my email and we can transfer the files that way.

**OstanNick** · 07-03-2014, 10:20 AM

Sure, I can e-mail them to you -- since the text files are >5mb and the limit here is <20kb

**OstanNick** · 07-10-2014, 06:34 AM

I 'figured it out'. May have been a stupid thing to do on my end, but basically the whitelist must be generated as the smrtanalysis user. Make sure you do the following:

Code:

su smrtanalyis

Code:

> enter password

Code:

/usr/local/bin/python.decon$ python whitelist.py 147_woot.align 81740 > /opt/smrtanalysis/data/147/whitelist.txt

Note the space between the '>' and the beginning of the directory. It didn't work when I didn't include the space.

Once the file is created, do not change the permissions whatsoever (chmod/chown), or it will not work. I was changing the permissions on the file to be readable/writeable by all users which I think was the problem.

Cheers,
Nick

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