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Old 01-24-2018, 05:50 AM   #1
echo manolis
Junior Member
Location: Italy

Join Date: Jan 2018
Posts: 6
Default GATK4, bash script... step CreateSequenceGroupingTSV

Ubuntu, Bash 4.2.25


I copy and paste the code about CreateSequenceGroupingTSV and in this way I created a python file...
When I'm going to run it I have the following error:

:~/GATK4/IlluminaExomePairEnd/0.pipe$ python

File "", line 31
hg38_protection_tag = ":1+"
IndentationError: unindent does not match any outer indentation level
the ^ symbol is under the last ", after +

Any help to fix it!?

Many thanks,
echo manolis is offline   Reply With Quote
Old 01-24-2018, 01:06 PM   #2
Location: MA, USA

Join Date: Feb 2014
Posts: 58

Hi M,

In python, whitespace is very important - this is how code blocks are separated ("indentation level" in the error). I'd guess that when you copy and pasted the script, the spaces or tabs around the code was lost.

You could have a look at the original version and make sure that your version has the same number of spaces before each bit of code. Or you could download the python script (rather and copy and paste) which may preserve the whitespace.


neavemj is offline   Reply With Quote


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