BioNanoAnalyst - KeyError

[AlanTracey99]

I get the following error a couple of minutes after setting BioNanoAnalyst running. It seems to be due to be something to do with contig IDs.

Process Process-31:
Traceback (most recent call last):
File "/software/pathogen/external/apps/usr/local/Python-2.7.13/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
self.run()
File "/software/pathogen/external/apps/usr/local/Python-2.7.13/lib/python2.7/multiprocessing/process.py", line 114, in run
self._target(*self._args, **self._kwargs)
File "/software/pathogen/external/apps/usr/local/BioNanoAnalyst-20170928/scripts/Analysis.py", line 345, in alignedInf
name = self.ref_id[RefCtgId]
KeyError: 67

Here are my 13 scaffold fasta headers:

Super-Scaffold_1
Super-Scaffold_2
Super-Scaffold_3
Super-Scaffold_4
Super-Scaffold_5
Super-Scaffold_7
Super-Scaffold_10
Super-Scaffold_11
Super-Scaffold_12
Super-Scaffold_67
Super-Scaffold_70
Super-Scaffold_72
Super-Scaffold_133

And the first 3 columns of my xmap file:

#f int int
1 1 1
2 2 2
3 3 3
4 4 4
5 69 4
6 5 5
7 9 7
8 7 7
9 8 7
10 10 10
11 11 11
12 136 12
13 12 12
14 67 67
15 70 70
16 202 70
17 72 72
18 133 133

[yyx8671]

Hi @AlanTracey99,

It seems your 'RefContigID' in your xmap file is the super_scaffold ID. To my understanding, the 'RefContigID' is calculated from 1 to the last header, for instance Super-Scaffold_1 should be RefContigID 1 and Super-Scaffold_133 should be RefContigID 13. In your case, they don't math with each other and error raised.

[AlanTracey99]

Hi Andy That's right. What I don't understand is why they don't match up. Do you have some data that we could take a look at please? Is there something we need to do to our sequence fasta headers before running BioNanoAnalyst to make the naming acceptable? Thanks, Alan

…

On Thu, Oct 19, 2017 at 4:10 PM, Andy Yuan ***@***.***> wrote: Hi @AlanTracey99 <https://github.com/alantracey99>, It seems your 'RefContigID' in your xmap file is the super_scaffold ID. To my understanding, the 'RefContigID' is calculate from 1 to the last header, for instance Super-Scaffold_1 should be RefContigID 1 and Super-Scaffold_133 should be RefContigID 13. In your case, they don't math with each other and error raised. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AcggGd2jf-bO99KBmsA9Y9tbm66xq576ks5st2ZVgaJpZM4P6ziF> .

[yyx8671]

Hi Alan,
I'm not sure how did you get your xmap file. If you don't mind, you may try our another script: https://github.com/appliedbioinformatics/runBNG to regenerate your xmap file and try BioNanoAnalyst again.

We have also provided a test file and you can have a test.

Cheers,
Andy

[AlanTracey99]

Hi Andy Thanks for this. I've attempted to run runBNG, but it hasn't produced an xmap file. The only files I have are:

…

-rw-r--r-- 1 alt hsg 4255 Sep 20 18:34 Hmic.stdout -rw-r--r-- 1 alt hsg 130695 Sep 20 18:34 Hmic.rmap -rw-r--r-- 1 alt hsg 1125 Sep 20 18:34 Hmic_repeatStats.txt I'm not sure where to go next with this.... Thanks, Alan

On Thu, Oct 19, 2017 at 6:17 PM, Andy Yuan ***@***.***> wrote: Hi Alan, I'm not sure how did you get your xmap file. If you don't mind, you may try our another script: https://github.com/appliedbioinformatics/runBNG to regenerate your xmap file and try BioNanoAnalyst again. We have also provided a test file and you can have a test. Cheers, Andy — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AcggGTlkRabYxddjAjoG64WZLSiIVaM3ks5st4QogaJpZM4P6ziF> .