Hi, 

I am learning STAR using two sets of 1000 RNA-seq reads and mapping to the human genome.

But am having a problem: When the STAR mapping run finishes no Alignemnt.out.sam file is created.

I am using the following:


/home/programs/STAR-STAR_2.4.2a/bin/Linux_x86_64_static/STAR \  
--runMode alignReads \  
--limitGenomeGenerateRAM 31000000000 \  
--limitIObufferSize 150000000 \  
--genomeDir /home/test_index \  
--runThreadN 8 \  
--outFilterMismatchNmax 2 \  
--outFilterMultimapNmax 10 \  
--genomeLoad NoSharedMemory \  
--alignIntronMin 21 \  
--outStd SAM \  
--outSAMattributes Standard \  
--outSJfilterReads Unique \  
--sjdbGTFfile /home/gene_models/Homo_sapiens.GRCh38.76.gtf \  
--readFilesIn /home/reads/short_reads_human.fastq /home/ddowling/lsf_test/short_reads_human_2.fastq 

  

STAR finishes and creates the following files in the working directory:


_STARgenome  
SJ.out.tab  
Log.std.out  
Log.progress.out  
Log.out  
Log.final.out  


The 'Alignment.out.sam' is missing.



The Log.std.out reads:

14:21:23 ..... Started STAR run  
14:21:23 ..... Loading genome  
14:22:21 ..... Processing annotations GTF  
14:22:49 ..... Inserting junctions into the genome indices  
14:25:03 ..... Started mapping  
14:25:13 ..... Finished successfully  



So I am unsure where the problem is.


Thank you.



You used --outStd SAM, which would have outputted the Aligned.out.bam file to your stdout.

From [the docs][1]:

> --outStd default: Log string: which output will be directed to stdout (standard out) SAM:  alignments in SAM format (which normally are
> output to Aligned.out.sam file), normal standard output will go into
> Log.std.out

So check the other log files for a SAM file, and if it's not there, read the manual next time! (and be glad you didn't make the same mistake with a much slower aligner ;)

EDIT: But upvote for your question because you asked it excellently :)
 [1]: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf