FATAL ERROR when using --parameterFiles

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Babak A

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Jun 19, 2022, 5:27:15 PMJun 19
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Hi Alex,

I am trying to use a parametersFiles, however, STAR cannot parse parameters from this file. Even when I use the ENCODE.txt parameters, I get the following error:

EXITING: FATAL INPUT ERROR: unrecognized parameter name "--outFilterType" in input "/path/to/file/ENCODE.txt" 
SOLUTION: use correct parameter name (check the manual)

I am really not sure why STAR cannot parse and use this file. I tried multiple STAR versions, including 2.7.10a_alpha_220601.

Thanks,
Babak  

Babak A

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Jun 19, 2022, 11:01:45 PMJun 19
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It seems the workaround is to remove the double-dash "--" from the argument names.

Babak

Alexander Dobin

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Jul 12, 2022, 12:35:55 PMJul 12
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Hi Babak,

sorry for the delayed reply. Yes, that correct - the double dashes are only used on the command line, in a "parameters" file each parameter has to start from a new line without double dashes.

Cheers
Alex

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