Hello, I am trying to align RNA sequencing data from the NCBI SRA database to the Apis mellifera genome with STAR. The alignment worked fine. However, the mapping step of the alignment seems to be a bit slow. Furthermore, increasing the number of available threads does not improve the speed. Below you can find the command I used and the content of the Log.final.out file. Is this a good speed for STAR? Are there any methods to improve the speed?
STAR --runThreadN 12 --genomeDir ~/scratch/genomeDir --readFilesIn $word_1.fastq $word_2.fastq --outFileNamePrefix $word --outSAMtype BAM SortedByCoordinate --outSAMattrRGline ID:$word SM:$sample PL:ILLUMINA Started job on | Nov 20 12:44:12 Started mapping on | Nov 20 12:44:12 Finished on | Nov 20 12:57:25 Mapping speed, Million of reads per hour | 52.40 Number of input reads | 11542556 Average input read length | 150 UNIQUE READS: Uniquely mapped reads number | 10873607 Uniquely mapped reads % | 94.20% Average mapped length | 149.74 Number of splices: Total | 3605561 Number of splices: Annotated (sjdb) | 0 Number of splices: GT/AG | 3574735 Number of splices: GC/AG | 23103 Number of splices: AT/AC | 1720 Number of splices: Non-canonical | 6003 Mismatch rate per base, % | 0.46% Deletion rate per base | 0.03% Deletion average length | 2.17 Insertion rate per base | 0.02% Insertion average length | 1.90 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 299041 % of reads mapped to multiple loci | 2.59% Number of reads mapped to too many loci | 2889 % of reads mapped to too many loci | 0.03% UNMAPPED READS: Number of reads unmapped: too many mismatches | 0 % of reads unmapped: too many mismatches | 0.00% Number of reads unmapped: too short | 364700 % of reads unmapped: too short | 3.16% Number of reads unmapped: other | 2319 % of reads unmapped: other | 0.02% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00%