kSNP / Discussion / General Discussion: Error while running kSNP4

Abed Kurdi - 2023-08-18

Hello there,

I am facing a problem while trying to run kSNP4. I am using the following command:
kSNP4 -k 11 -outdir kSNP_output/ -in input_for_kSNP.in -vcf -NJ -core -ML -CPU 50

The program reaches (2/10) Running jellyfish to get kmer counts for few seconds and it stops. It is throwing the following error:
DEBUG:Waiting for dumpers and frequency checkers to finish Traceback (most recent call last): File "inline_frequency_check.py", line 97, in <module> File "inline_frequency_check.py", line 79, in getMinKmerCoverage File "statistics.py", line 311, in mean TypeError: 'NoneType' object is not iterable

Any idea what is going on?

Thank you in advance!

Last edit: Abed Kurdi 2023-08-18

If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
- Barry G. Hall - 2023-08-18
  
  File names may contain only A-Z a-Z 0-1 _ and - characters. Your output file name kSNP_output/ contains the / character.
  
  Try getting rid of the / character.
  
  Barry G. Hall
  Director, Bellingham Research Institute
  barryghall@gmail.com
  http://www.bellinghamresearch.com http://www.bellinghamresearch.com/
  
  On Aug 18, 2023, at 2:41 AM, Abed Kurdi abedkurdi@users.sourceforge.net wrote:
  
  Hello there,
  
  I am facing a problem while trying to run kSNP4. I am using the following command:
  kSNP4 -k 11 -outdir kSNP_output/ -in input_for_kSNP.in -vcf -NJ -core -ML -CPU 50
  
  The program reaches (2/10) Running jellyfish to get kmer counts for few seconds and it stops. It is throwing the following error:
  DEBUG:Waiting for dumpers and frequency checkers to finish Traceback (most recent call last): File "inline_frequency_check.py", line 97, in <module> File "inline_frequency_check.py", line 79, in getMinKmerCoverage File "statistics.py", line 311, in mean TypeError: 'NoneType' object is not iterable</module>
  
  Any idea what is going on?
  
  Thank you in advance!
  
  Error while running kSNP4 https://sourceforge.net/p/ksnp/discussion/general/thread/15fae4c9c2/?limit=25#8065
  Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/ksnp/discussion/general/
  
  To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
  
  PastedGraphic-1.pdf
  
  alternate
  
  If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
  - Abed Kurdi - 2023-08-19
    
    Dear Barry,
    I tried to run it again without the backslash and it did not work.
    
    If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
    - Barry G. Hall - 2023-08-19
      
      Please email me directly at the address in the “Troubleshooting kSNP4.1 (or kSNP4)” document that was included in the package you downloaded. Answer All of the questions in that document or I will ignore your request for support.
      
      Barry G. Hall
      Director, Bellingham Research Institute
      barryghall@gmail.com
      http://www.bellinghamresearch.com http://www.bellinghamresearch.com/
      
      On Aug 19, 2023, at 6:55 AM, Abed Kurdi abedkurdi@users.sourceforge.net wrote:
      
      Dear Barry,
      I tried to run it again without the backslash and it did not work.
      
      Error while running kSNP4 https://sourceforge.net/p/ksnp/discussion/general/thread/15fae4c9c2/?limit=25#8065/20d3/1415
      Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/ksnp/discussion/general/
      
      To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
      
      PastedGraphic-1.pdf
      
      alternate
      
      If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

Eric Fournier - 2023-09-27

Hi Abed,

do you receive a response regarding your problem. I got exactly the same error.

Best,
Eric Fournier
Bioinformatician, LSPQ

If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

Error while running kSNP4

kSNP4 does SNP discovery and SNP annotation from whole genomes

Forums

Help

Error while running kSNP4

Error while running kSNP4

kSNP4 does SNP discovery and SNP annotation from whole genomes

Forums

Help

Error while running kSNP4 document.SUBSCRIPTION_OPTIONS = { "thing": "topic", "subscribed": false, "url": "subscribe", "icon": { "css": "fa fa-envelope-o" } };

Error while running kSNP4