STAR producing an empty BAM file

Question

[oldtownroald]

I'm trying to run STAR but I am getting an empty BAM file. Does anyone know why this is happening and how to fix it?

iCount mapstar demultiplexed/demux_NNNGGCGNN.fastq.gz hs88 mapping_NNNGGCGNN \
> --annotation homo_sapiens.88.gtf.gz 
#for context, mapstar needs the following arguments reads, genome_index, out_dir

iCount mapstar demultiplexed/demux_NNNGGCGNN.fastq.gz hs88 mapping_NNNGGCGNN --annotation homo_sapiens.88.gtf.gz
Input parameters for function 'map_reads' in iCount.externals.star
    reads: demultiplexed/demux_NNNGGCGNN.fastq.gz
    genome_index: hs88
    out_dir: mapping_NNNGGCGNN
    annotation: homo_sapiens.88.gtf.gz
    multimax: 10
    mismatches: 2
    threads: 1
    genome_load: False
Mapping reads from demultiplexed/demux_NNNGGCGNN.fastq.gz
Nov 02 20:23:11 ..... started STAR run
Nov 02 20:23:11 ..... loading genome
Nov 02 20:23:12 ..... processing annotations GTF
Nov 02 20:23:32 ..... inserting junctions into the genome indices
Nov 02 20:23:34 ..... started mapping
Done.

[Ram]

1. What is hs88? It doesn't look like a common human genome version
2. You're not running STAR, you're running something that's internally running STAR. It's not the same as running STAR directly.

[vkkodali_ncbi]

What do you see in the log files in the directory mapping_NNNGGCGNN, specifically Log.out file?

[VD]

Hi, did you eventually spot the problem?