Question: Error while running STAR aligner
0
gravatar for XBria
3.3 years ago by
XBria70
germany
XBria70 wrote:

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 • 2.5k views
ADD COMMENTlink modified 3.3 years ago by GenoMax96k • written 3.3 years ago by XBria70

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

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by GenoMax96k

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

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by XBria70
1

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

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by GenoMax96k

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

Many thanks for the hint !

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by XBria70

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 REPLYlink modified 3.3 years ago • written 3.3 years ago by XBria70
1

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 REPLYlink written 3.3 years ago by Devon Ryan98k

Killed

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

ADD REPLYlink written 3.3 years ago by WouterDeCoster45k

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 REPLYlink modified 3.3 years ago • written 3.3 years ago by XBria70
1

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 REPLYlink written 3.3 years ago by GenoMax96k
2

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

ADD REPLYlink written 3.3 years ago by michael.ante3.6k
1

You can check the memory usage of the process using htop or top.

ADD REPLYlink written 3.3 years ago by WouterDeCoster45k
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