Hello all,

I'm attempting to use STAR to map some RNA-seq data, but keep getting some sort of error. Here is the command I used:

for i in `ls *_clean.fastq | sed 's/_clean.fastq//'`; do STAR --runThreadN 20 --quantMode GeneCounts --outFileNamePrefix aligned_haploid/$i --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --genomeDir /media/smasher/4TB_data/pairwise_brb_8-2023/haploid_genome --readFilesIn $i\_clean.fastq; done

Here's the error I get:

EXITING because of FATAL ERROR: failed reading from temporary file: aligned_haploid/A01_STARtmp//BAMsort/2/44

It doesn't happen to every fastq file, I mapped 95 files and 5 of them generated this error. I thought maybe it was something to do with the fastq's themselves because I mapped them individually rather than in a loop and still got this same error. However, when I map them to a different, but very similar, genome, I get the error but for different files.

Anyone know what's going on here and have an idea of how to fix it? I'm running STAR 2.7.10a via Mamba, could that be the problem?

Thanks!