Error during mapping to mitochondrial genome

[desmodus1984]

Hi,

I am interested in testing differential mitochondrial gene expression on different temperatures. I indexed the mitogenome, using the following code:

STAR --runThreadN 8 \ --runMode genomeGenerate \ --genomeDir /home/Bilova/ \ --genomeFastaFiles /home/juaguila/Bilova.fasta \ --genomeSAindexNbases 6 \ --sjdbGTFfile /home/juaguila/Bilova.gtf \ --sjdbOverhang 49

And then started mapping using:

STAR --runThreadN 10 \ --genomeDir /home/Bilova/ \ --readFilesIn ${base}_1_val_1.fq ${base}_2_val_2.fq \ --outFileNamePrefix ${base} \ --outSAMtype BAM SortedByCoordinate \ --outSAMattributes NH HI NM MD \ --alignIntronMin 20 \ --alignIntronMax 100 \ --quantMode GeneCounts

I checked the log file, and it shows an error:

STAR version: 2.7.10b   compiled: 2022-11-01T09:53:26-04:00 :/home/dobin/data/STAR/STARcode/STAR.master/source

Sep 04 20:16:35 ..... started STAR run Sep 04 20:16:35 ..... loading genome Sep 04 20:16:35 ..... started mapping Sep 04 20:30:13 ..... finished mapping Sep 04 20:30:14 ..... started sorting BAM

EXITING because of fatal ERROR: not enough memory for BAM sorting: SOLUTION: re-run STAR with at least --limitBAMsortRAM 1001750809 Sep 04 20:30:14 ...... FATAL ERROR, exiting

STAR --runThreadN 10 --genomeDir /home/Bilova/ --readFilesIn 101.V01347.R1_1_val_1.fq 101.V01347.R1_2_val_2.fq --outFileNamePrefix 101.V01347.R1 --outSAMtype BAM SortedByCoordinate --outSAMattributes NH HI NM MD --alignIntronMin 20 --alignIntronMax 100 --quantMode GeneCounts STAR version: 2.7.10b compiled: 2022-11-01T09:53:26-04:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Sep 04 20:30:14 ..... started STAR run Sep 04 20:30:14 ..... loading genome Sep 04 20:30:14 ..... started mapping Sep 04 20:55:23 ..... finished mapping Sep 04 20:55:23 ..... started sorting BAM

EXITING because of fatal ERROR: not enough memory for BAM sorting: SOLUTION: re-run STAR with at least --limitBAMsortRAM 1004207550

I wanted to inquire because I am confused, it prompted an error, when I checked the directory I can find the expected files. -rw-r--r-- 1 juaguila hpc_jfierst 0 Sep 4 20:16 100.V01919.R1Aligned.sortedByCoord.out.bam -rw-r--r-- 1 juaguila hpc_jfierst 1652 Sep 4 20:30 100.V01919.R1Log.progress.out -rw-r--r-- 1 juaguila hpc_jfierst 0 Sep 4 20:30 101.V01347.R1Aligned.sortedByCoord.out.bam drwx------ 3 juaguila hpc_jfierst 4096 Sep 4 20:30 100.V01919.R1_STARtmp -rw-r--r-- 1 juaguila hpc_jfierst 34 Sep 4 20:30 100.V01919.R1SJ.out.tab -rw-r--r-- 1 juaguila hpc_jfierst 650 Sep 4 20:30 100.V01919.R1ReadsPerGene.out.tab -rw-r--r-- 1 juaguila hpc_jfierst 6828 Sep 4 20:30 100.V01919.R1Log.out

I am asking, because I don't know if the gene counts are reliable despite the "not enough memory for BAM sorting" error.

Thanks;