Entering edit mode
7 weeks ago
luzglongoria ▴ 40
I'm using STAR with a small genome. My samples are paired. The commands are:
For genome indexes
STAR --runThreadN 20 --runMode genomeGenerate --genomeDir /path/to/folder/Analyses/STAR/ --genomeFastaFiles /path/to/genome_reference/genome.fna --readFilesCommand zcat path/to/folder/with/giz_samples/R1.fq.gz R2.fq.gz --sjdbGTFfile path/to/genome_reference/genome.gff --genomeSAindexNbases 11
For mapping (run in the folder where samples are)
STAR --runThreadN 30 --genomeDir /genomeDir/path/to/folder/Analyses/STAR/ --readFilesCommand zcat --readFilesPrefix path/to/folder/with/giz_samples/ --readFilesIn R1.fq.gz R2.fq.gz --outFileNamePrefix /path/to/folder/Analyses/STAR/Alignment/
The problem is that when I go to the folder "Alignment" (
/path/to/folder/Analyses/STAR/Alignment/) there is a Aligned.out.sam file but it has a sample size of 16321 and it does not increase even after hours.
If I check the file
Log.progress.out there is an empty table.
If I do:
head -20 Aligned.out.sam
Then I get
@HD VN:1.4 @SQ SN:NC_041679.1 LN:721917 @SQ SN:NC_041680.1 LN:680232 @SQ SN:NC_041681.1 LN:617973 @SQ SN:NC_041682.1 LN:707398 @SQ SN:NC_041683.1 LN:690376 @SQ SN:NC_041684.1 LN:795041 @SQ SN:NC_041685.1 LN:1287098 @SQ SN:NC_041686.1 LN:1283005 @SQ SN:NC_041687.1 LN:1693561 @SQ SN:NC_041688.1 LN:1164052 @SQ SN:NC_041689.1 LN:1833711 @SQ SN:NC_041690.1 LN:2613071 @SQ SN:NC_041691.1 LN:1960421 @SQ SN:NC_041692.1 LN:2600757 @SQ SN:NW_021628359.1 LN:109844 @SQ SN:NW_021628360.1 LN:3880 @SQ SN:NW_021628362.1 LN:3821 @SQ SN:NW_021628363.1 LN:3789 @SQ SN:NW_021628364.1 LN:20763
I have run in this server STAR and it works fine.
Does anyone know what's going on in here?
Thank you in advance.
I have tried reducing the number of threads but it is the same.
You are not running out of storage quota on the particular disk?
If I do
then I get
So it not full at all
Is this a server administered by a sys admin? Do you know if individual user accounts have "quota"?
If your user account has a storage quota/limit and once you get past it, programs are not allowed to write to the disk. If quota's are present generally you should get an email indicating that you are close to or over it. Even if the disk is not full, if your account has reached its quota then no writes are possible.
Thanks for your reply.
It is not a problem of memory since I can run other mapping analyses with no problem (I get big Sam output files with no problem).
This issue only happens when running STAR.
Memory =/= disk storage.
Likely you will need to diagnose this yourself since we don't have access to your data/server. Your command obviously is ok since it starts making the SAM file. I am not a regular
STARuser so I don't know if
STARwrites non-aligning reads to alignment file. If it only stores reads that align then perhaps none of your reads are aligning to this genome.