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Old 10-06-2014, 02:33 PM   #1
Junior Member
Location: Cleveland

Join Date: Aug 2014
Posts: 4
Default error running STAR

I am using STAR to map my paired end rna seq data. I keep running into the following error msg.
EXITING because of FATAL ERROR in input reads: unknown file format: the read ID should start with @ or >
This was my command line:
-bash-3.2$ /pathToStarDir/ STAR --genomeDir /pathToGenome/ --readFilesCommand zcat --readFilesIn /pathToFile/587352_1_1.fastq.gz pathToFile/587352_1_2.fastq.gz --runThreadN 3

When I zless my .fastq.gz file to check the format of the file, the first few lines looks like this:

Has anyone ran into similar problems before? Is it a file problem or there was mistakes in my command ?

Thanks for the help in advance.

JJZ is offline   Reply With Quote
Old 10-06-2014, 04:12 PM   #2
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,101

Can you try Brian's tool to see if you can fix problems with your fastq files: I am not sure if it will catch malformed ID headers.

Alternatively fastqValidator can be used to see if you do have a problem with formatting:
GenoMax is offline   Reply With Quote
Old 10-06-2014, 05:31 PM   #3
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

I don't see a problem with the first 8 lines, at least. And yes, requires correctly-formatted fastq headers; it's only for fixing broken pair ordering. I'm not familiar with how STAR deals with gzipped files, but perhaps you could try decompressing it first?
Brian Bushnell is offline   Reply With Quote

error, file format, star

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