Error while running STAR aligner

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6.5 years ago

XBria ▴ 90

Hi,

I am trying to run STAR to map. The code is :

    STAR --runThreadN 8 --genomeDir /home/XBria/bin/chrX.fa  --sjdbGTFfile /home/ 
XBria /my_rnaseq_exp/chrX_data/genes/chrX.gtf  --readFilesIn /home/ 
XBria /my_rnaseq_exp/chrX_data/samples/ERR188044_chrX_1.fastq.gz   /home/ 
XBria /my_rnaseq_exp/chrX_data/samples/ERR188044_chrX_2.fastq.gz --outFileNamePrefix STAR

result:

Nov 28 19:35:54 ..... started STAR run
Nov 28 19:35:54 ..... loading genome

EXITING because of FATAL ERROR: could not open genome file /home/XBria/bin/chrX.fa/genomeParameters.txt
SOLUTION: check that the path to genome files, specified in --genomeDir is correct and the files are present, and have user read permsissions

Nov 28 19:35:54 ...... FATAL ERROR, exiting

I drag the chrX.fa and forward and reverse reads files into the terminal. Any advice is appreciated.

Thanks.

RNA-Seq • 4.2k views

ADD COMMENT • link updated 6.5 years ago by GenoMax 142k • written 6.5 years ago by XBria ▴ 90

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Looks like you have spaces in several file paths? (or is that just a side effect of copy-paste?) Remove those.

ADD REPLY • link 6.5 years ago by GenoMax 142k

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I just edited and tested. Unfortunately the same error occurs !

ADD REPLY • link 6.5 years ago by XBria ▴ 90

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Have you created STAR genome index (in this case for chrX) already?

ADD REPLY • link 6.5 years ago by GenoMax 142k

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Oops. no! I 'm trying to run with the Hisat indices I've already mapped !

Many thanks for the hint !

ADD REPLY • link 6.5 years ago by XBria ▴ 90

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Dear Genomax,

I run making indices and got the following :

Nov 28 20:12:02 ..... started STAR run Nov 28 20:12:02 ... starting to generate Genome files Nov 28 20:12:04 ... starting to sort Suffix Array. This may take a long time... Nov 28 20:12:05 ... sorting Suffix Array chunks and saving them to disk... Killed

Is it done right !!

ADD REPLY • link 6.5 years ago by XBria ▴ 90

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Well, it's "done" in that it's not running, but the "Killed" means that your system killed it. I'm guessing that you ran out of memory.

ADD REPLY • link 6.5 years ago by Devon Ryan 104k

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Killed

That doesn't look right. Do you have sufficient memory available?

ADD REPLY • link 6.5 years ago by WouterDeCoster 47k

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I am not indexing a large file. it is only chrX ! RAM of the system is 8G. fa file is 158 and GTF is 7 MB ! Are they still too much ?

ADD REPLY • link 6.5 years ago by XBria ▴ 90

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I think there are some tricks to make the indexing work if you have less RAM if I recall right. Search for STAR genome index threads here. You may need to use one of those workarounds.

ADD REPLY • link 6.5 years ago by GenoMax 142k

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After sorting out the memory issue, you should also add the parameter --readFilesCommand zcat , since your fastq files are zipped.