STAR aligner -- Alignment.out.sam missing

Question

[ddowlin]

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.

Answer 1

[John]

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

From the docs:

--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 :)