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MHH-RCUG / Wochenende

Deprecated see https://github.com/MHH-RCUG/nf_wochenende : A whole Genome/Metagenome Sequencing Alignment Pipeline in Python3
https://github.com/MHH-RCUG/nf_wochenende
MIT License
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wochenende plot error b: exotic headers ? #84

Closed colindaven closed 3 years ago

colindaven commented 4 years ago

Project 2020_035351

Traceback (most recent call last):
  File "wochenende_plot.py", line 450, in <module>
    organism4=i.split("_")[6]
IndexError: list index out of range
Traceback (most recent call last):
  File "wochenende_plot.py", line 450, in <module>
    organism4=i.split("_")[6]
IndexError: list index out of range
colindaven commented 3 years ago

Also here:

/ngsssd1/rcug/wochenende_test/pilz/plots$ bash runbatch_wochenende_plot.sh Traceback (most recent call last): File "wochenendeplot.py", line 450, in organism4=i.split("")[6] IndexError: list index out of range

colindaven commented 3 years ago

@poer-sophia Can you please have a look to see if you can reproduce this error ? The plotting needs to be rewritten/ refactored into methods, but to start with can you please

a) clone the dev branch (or better download and make an internal git repo with the plotting code only)

b) Try to replicate the error

c) Add try/ catch statements to catch and output error lines and make parsing safer (this was a different reference to that which the program was originally written for).

Thanks, Colin

colindaven commented 3 years ago

Being done in local repo