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Old 02-19-2019, 08:52 AM   #1
NDUFB11
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Default STAR read Mapping

Hello everybody,

I kindly need your help again ...

I want to map my reads on the genome using STAR but for some reason I get an error that I don't know how to solve

When I type the command line here is what I get:



Code:
Patrizios-MBP:processing patrizio$ STAR --genomeDir genome/star/ --runThreadN 4 --readFilesIn clipped/SRR359063_1.fastq.zip clipped/ SRR359063_2.fastq.zip --outFileNamePrefix mapping/star/SRR359063. --outSAMattributes All --outSAMtype BAM SortedByCoordinate --readFileCommand gunzip
EXITING: FATAL INPUT ERROR: unrecoginzed parameter name "readFileIn" in input "Command-Line-Initial"
SOLUTION: use correct parameter name (check the manual)

Feb 19 18:49:56 ...... FATAL ERROR, exiting[/B]

I also tried to process unzipped files and remove the command to execute each single input file --readFileCommand, but still I can't go further,

I have a MacOs terminal,


thank you

Patrizio

Last edited by GenoMax; 02-19-2019 at 09:16 AM. Reason: Added [code] tags
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Old 02-19-2019, 08:57 AM   #2
GenoMax
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STAR requires a lot of RAM depending on genome size. e.g. human genome will need ~30G of free RAM which you may not have available on your Mac. If that is true, you will not be able to do this on your local mac.
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Old 02-19-2019, 09:04 AM   #3
NDUFB11
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Do you think that this is the reason why I have this error? this is a nematode genome so I thought the process would have been faster than human

I will scan the command, I found an error probably I didn't type correctly the command

later I will also try with topHat, it should be feasible because requires less RAM

thank you

Last edited by NDUFB11; 02-19-2019 at 09:07 AM.
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Old 02-19-2019, 09:15 AM   #4
GenoMax
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Oops. I should have looked at the error carefully. You are correct.

Edit: Found the problem. You have a space between clipped and file name here (clipped/ SRR359063_2.fastq.zip ). Remove that.
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Old 02-19-2019, 09:26 AM   #5
NDUFB11
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It's working !!!! holeee'!

have a look

Code:
Patrizios-MBP:processing patrizio$ STAR --genomeDir genome/star/ --runThreadN 4 --readFilesIn clipped/SRR359063_1.fastq clipped/SRR359063_2.fastq --outFileNamePrefix mapping/star/SRR359063. --outSAMattributes All --outSAMtype BAM SortedByCoordinate 
Feb 19 19:22:44 ..... started STAR run
Feb 19 19:22:44 ..... loading genome
Feb 19 19:22:49 ..... started mapping
Feb 19 19:23:50 ..... finished mapping
Feb 19 19:23:50 ..... started sorting BAM
Feb 19 19:23:54 ..... finished successfully
Patrizios-MBP:processing patrizio$
I can go further with the process !

Thank you GenoMax

at some point I will ship a bottle of wine to you

-P

Last edited by GenoMax; 02-19-2019 at 09:33 AM. Reason: Added [code] tags
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Old 02-19-2019, 09:34 AM   #6
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Looks good!
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