STAR segmentation fault (--genomeSAindexNbases not reassigning?)

[Anna Sappington]

Hello!

I have used STAR successfully in the past to align with large reference genomes. I am now trying to align with a small genome (~3230 bases). I am using STAR v. 2.4.1d (and have tried the older v. 2.3.0e) and have tried to set the --genomeSAIndexNbases parameter so as to accommodate the small genome. However, I am still receiving segmentation fault (core dumped) errors and when looking at the Log.out file, see that the --genomeSAIndexNbases is being recognized as 14 (the default) rather than the 4 or 5 I have tried to set it to based on log2(numBases)/2 -1 (the formula STAR provides).

Any suggestions would be much appreciated! And thanks in advance.

-Anna

[Alexander Dobin]

Hi Anna,

please try to set it even lower, to 3 or 2. If it does not work, please send me the Log.out file.

Cheers

Alex

[Anna Sappington]

Hi Alex, thanks so much for getting back to me.

I tried with 2 and 3 and am still getting the segmentation fault. I've attached the Log.out and will paste my script below:

/home/software/star/star-2.4.1d/bin/STAR --genomeDir /home/asapp/singleCellHBV/starReferenceGenome --genomeSAindexNbases 2 --readFilesIn /home/asapp/singleCellHBV/fastq/VyasUninf-H12_S480_comb_R1_001.fastq /home/asapp/singleCellHBV/fastq/VyasUninf-H12_S480_comb_R2_001.fastq --runThreadN 16 --outFileNamePrefix VyasUninf-H12_S480_comb_R2_001

It seems to be recognizing my other parameters (outFileNamePrefix, runThreadN, genomeDir, etc.), so unsure why it doesn't seem to set genomeSAindexNbases...

Thanks again for you help!
Anna

[Kirill Tsyganov]

Hi Anna, 

I think you are not using `--genomeSAindexNbases` in the right place.. That flag is for Genome Generation i.e for when you are making an index and not for the actual alignment step ! When you have small reference genome you need to account for it during "genome generation" i.e indexing step

So it should be something like this:

Step 1: Make index

```

STAR --runThreadN 16 \

            --runMode genomeGenerate \

            --genomeDir /path/to/your/starIndex/directory\

            --genomeFastaFiles /your/reference/file

            --genomeSAindexNbases 3

```

I'm sure you are aware of this but make sure that your "starIndex-directory" is premade, as STAR doesn't make it !

And backslashs are just BASH convention to span multiple lines.

Step 2 : Alignment 

```

STAR --runThredN 16 \

          --genomeDir /your/starIndex/directory \

          --readFilesIn /your/FASTQ/files \

          --outFileNamePrefix /your/fileNamePrefix 

```

This is what I think at least, Alex might clarify whether you can or can't use `--genomeSAindexNbases` during alignment step.

Cheers, 

Kirill 

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[Anna Sappington]

Ah yes, this was exactly it! Thank you very much for your detailed response!

Best,
Anna

[Kirill Tsyganov]

No probs, glad the issue was resolved.