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NDUFB11 02-19-2019 08:52 AM

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:


Patrizios-MBP:processing patrizio$ STAR --genomeDir genome/star/ --runThreadN 4 --readFilesIn clipped/ clipped/ --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


GenoMax 02-19-2019 08:57 AM

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.

NDUFB11 02-19-2019 09:04 AM

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

GenoMax 02-19-2019 09:15 AM

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/ ). Remove that.

NDUFB11 02-19-2019 09:26 AM

It's working :D :D :D !!!! holeee'!

have a look


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 :D


GenoMax 02-19-2019 09:34 AM

Looks good!

yoderto 10-22-2019 09:28 AM

Just a quick comment-- STAR does come with RAM limiting arguments: --limitGenomeGenerateRAM, --limitIObufferSize , --genomeSAsparseD

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