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Old 03-26-2019, 06:46 PM   #1
Location: Italy

Join Date: Jul 2017
Posts: 34
Default STAR Aligner quantMode and fatal error

Hello Everyone,

I have problems with STAR aligner.
I want to use the quantMode option in order to have .tab file that I will use for later analysis.

The first thing I did is the index of the genome:

STAR --runMode genomeGenerate --genomeDir genome/star/ --genomeFastaFiles /genome/Homo_sapiens.GRCh37.75.fa --sjdbGTFfile /genome/Homo_sapiens.GRCh37.75.gtf --runThreadN 20 --sjdbGTFtagExonParentTranscript Parent --sjdbGTFfeatureExon CDS --outFileNamePrefix genome/star/

from where I obtained this list of files

total 382248
-rw-rw-r--. 1        617 Mar 26 23:06 chrLength.txt
-rw-rw-r--. 1       1330 Mar 26 23:06 chrNameLength.txt
-rw-rw-r--. 1        713 Mar 26 23:06 chrName.txt
-rw-rw-r--. 1       919 Mar 26 23:06 chrStart.txt
-rw-rw-r--. 1      22187668 Mar 26 23:22
-rw-rw-r--. 1      21831277 Mar 26 23:22
-rw-rw-r--. 1     784390 Mar 26 23:22
-rw-rw-r--. 1        346597481 Mar 26 23:22 Log.out
drwx------. 2         6 Mar 26 23:05 _STARtmp
-rw-rw-r--. 1        0 Mar 26 23:22
then I run my sample

STAR --genomeDir genome/star --readFilesIn my_fastq/Treated_1_m1.fastq.gz my_fastq/Treated_1_m2.fastq.gz --outSAMtype BAM SortedByCoordinate --sjdbGTFfile genome/Homo_sapiens.GRCh37.75.gtf --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic –alignIntronMax 15000 --outFilterIntronMotifs RemoveNoncanonical --runThreadN 20 --sjdbGTFtagExonParentTranscript Parent --sjdbGTFfeatureExon CDS --outReadsUnmapped fastx --readFilesCommand zcat
and I have this error,

Mar 27 03:32:36 ..... started STAR run
Mar 27 03:32:36 ..... loading genome

EXITING because of FATAL ERROR: could not open genome file genome/star2/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

Mar 27 03:32:36 ...... FATAL ERROR, exiting

It seems like that he can not find the genomeParameters.txt file but was not even created during the indexing.

Does anybody had a similar problem or knows the solution?

Thank you for help

Last edited by NDUFB11; 03-26-2019 at 06:48 PM.
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