STAR is running but .sam file size does not increase after hours mapping

Question

[luzglongoria]

Hi there,

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.

[luzglongoria]

I have tried reducing the number of threads but it is the same.

[GenoMax]

You are not running out of storage quota on the particular disk?

[luzglongoria]

If I do

df -h

then I get

Filesystem                             Size  Used Avail Use% Mounted on
devtmpfs                               252G     0  252G   0% /dev
tmpfs                                  252G     0  252G   0% /dev/shm
tmpfs                                  252G   35M  252G   1% /run
tmpfs                                  252G     0  252G   0% /sys/fs/cgroup
/dev/mapper/vg_geneiousserver-lv_root  129G   15G  109G  12% /
/dev/sdh1                              9.8T  7.2T  2.2T  77% /home
/dev/sdc1                              477M  335M  113M  75% /boot
/dev/mapper/vg_data-home               2.0T  400G  1.5T  21% /var
/dev/mapper/vg_data-data               3.2T  2.6T  495G  84% /home2
tmpfs                                   51G   12K   51G   1% /run/user/42
tmpfs                                   51G     0   51G   0% /run/user/1005
tmpfs                                   51G     0   51G   0% /run/user/1044
tmpfs                                   51G     0   51G   0% /run/user/1028
tmpfs                                   51G     0   51G   0% /run/user/1067
tmpfs                                   51G     0   51G   0% /run/user/0

So it not full at all

[GenoMax]

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.

[luzglongoria]

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.

[GenoMax]

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 STAR user so I don't know if STAR writes non-aligning reads to alignment file. If it only stores reads that align then perhaps none of your reads are aligning to this genome.