STAR --genomeDir /mnt/d/NGS/rna-seq/03_ref  --outSAMunmapped Within  --outFilterType BySJout  --outSAMattributes NH HI AS NM MD  --outFilterMultimapNmax 20  --outFilterMismatchNmax 999  --outFilterMismatchNoverLmax 0.04  --alignIntronMin 20  --alignIntronMax 1000000  --alignMatesGapMax 1000000  --alignSJoverhangMin 8  --alignSJDBoverhangMin 1  --sjdbScore 1  --runThreadN 6  --genomeLoad NoSharedMemory  --outSAMtype BAM Unsorted  --quantMode TranscriptomeSAM  --outSAMheaderHD @HD VN:1.4 SO:unsorted  --outFileNamePrefix sub1-Ca13mCh-LGC9389_L1_PE_quals.temp/sub1-Ca13mCh-LGC9389_L1_PE_quals  --readFilesIn sub1-Ca13mCh-LGC9389_L1_1_cleaned.fq sub1-Ca13mCh-LGC9389_L1_2_cleaned.fq
Apr 26 10:56:19 ..... started STAR run
Apr 26 10:56:19 ..... loading genome

EXITING because of FATAL ERROR: could not open genome file /mnt/d/NGS/rna-seq/03_ref/genomeParameters.txt
SOLUTION: check that the path to genome files, specified in --genomeDir is correct and the files are present, and have user read permsissions

Apr 26 10:56:19 ...... FATAL ERROR, exiting
"STAR --genomeDir /mnt/d/NGS/rna-seq/03_ref  --outSAMunmapped Within  --outFilterType BySJout  --outSAMattributes NH HI AS NM MD  --outFilterMultimapNmax 20  --outFilterMismatchNmax 999  --outFilterMismatchNoverLmax 0.04  --alignIntronMin 20  --alignIntronMax 1000000  --alignMatesGapMax 1000000  --alignSJoverhangMin 8  --alignSJDBoverhangMin 1  --sjdbScore 1  --runThreadN 6  --genomeLoad NoSharedMemory  --outSAMtype BAM Unsorted  --quantMode TranscriptomeSAM  --outSAMheaderHD @HD VN:1.4 SO:unsorted  --outFileNamePrefix sub1-Ca13mCh-LGC9389_L1_PE_quals.temp/sub1-Ca13mCh-LGC9389_L1_PE_quals  --readFilesIn sub1-Ca13mCh-LGC9389_L1_1_cleaned.fq sub1-Ca13mCh-LGC9389_L1_2_cleaned.fq" failed! Plase check if you provide correct parameters/options for the pipeline!