STAR read Mapping

NDUFB11 · 02-19-2019, 09:52 AM

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

GenoMax · 02-19-2019, 09:57 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, 10:04 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, 10:15 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/ SRR359063_2.fastq.zip ). Remove that.

NDUFB11 · 02-19-2019, 10:26 AM

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

GenoMax · 02-19-2019, 10:34 AM

Looks good!

yoderto · 10-22-2019, 10:28 AM

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

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02-19-2019, 09:52 AM	#1
NDUFB11 Member Location: Italy Join Date: Jul 2017 Posts: 34	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 10:16 AM. Reason: Added [code] tags

02-19-2019, 10:04 AM	#3
NDUFB11 Member Location: Italy Join Date: Jul 2017 Posts: 34	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 10:07 AM.

02-19-2019, 09:57 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,087	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.

02-19-2019, 10:15 AM	#4
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,087	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.

02-19-2019, 10:34 AM	#6
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,087	Looks good!

10-22-2019, 10:28 AM	#7
yoderto Junior Member Location: Philadelphia Join Date: Feb 2019 Posts: 2	Just a quick comment-- STAR does come with RAM limiting arguments: --limitGenomeGenerateRAM, --limitIObufferSize , --genomeSAsparseD