/star.ht.sh: line 78: 20173-0002_S2_R1_001: value too great for base (error token is "0002_S2_R1_001")

[JianGuoZhou3]

Hi Alex, @alexdobin I have an error of STAR for single-end mRNA RNA-seq. (QuantSeq 3' mRNA-Seq Library Prep Kit FWD) I found the code from the web https://www.lexogen.com/quantseq-data-analysis/ So my code is belowed:

ln -s ${dir}/clean/${i}_trimmed_clean ${dir}/raw/${i}.fastq.gz
    nohup STAR \
    --runThreadN 30 \
    --genomeDir $star_index \
    --readFilesCommand zcat \
    --readFilesIn ${dir}/raw/${i}.fastq.gz \
    --outFilterType BySJout \
    --outFilterMultimapNmax 20 \
    --alignSJoverhangMin 8 \
    --alignSJDBoverhangMin 1 \
    --outFilterMismatchNmax 999 \
    --outFilterMismatchNoverLmax 0.1 \
    --alignIntronMin 20 \
    --alignIntronMax 1000000 \
    --alignMatesGapMax 1000000 \
    --outSAMattributes NH HI NM MD \
    --limitBAMsortRAM 10717148197 \
    --outSAMtype BAM SortedByCoordinate \
    --outFileNamePrefix ${dir}/CircRNA/STAR/${i}/${i}_

however, the nohup out was shown that:

20173-0001_S1_R1_001
93567
20173-0002_S2_R1_001
93568
20173-0003_S3_R1_001
ln: failed to create symbolic link ‘/home/zhou/t12b//RNA_seq/raw/20173-0001_S1_R1_001.fastq.gz’: File exists
ln: failed to create symbolic link ‘/home/zhou/t12b//RNA_seq/raw/20173-0002_S2_R1_001.fastq.gz’: File exists
Sep 05 20:26:35 ..... started STAR run
Sep 05 20:26:35 ..... started STAR run
Sep 05 20:26:35 ..... loading genome
Sep 05 20:26:35 ..... loading genome
Sep 05 20:47:52 ..... started mapping
Sep 05 20:47:52 ..... started mapping
Sep 05 20:52:23 ..... finished mapping
Sep 05 20:52:27 ..... finished mapping
Sep 05 20:52:28 ..... started sorting BAM
Sep 05 20:52:33 ..... started sorting BAM
Sep 05 20:52:41 ..... finished successfully
/home/zhou/t12b/RNA_seq/code/star.ht.sh: line 78: 20173-0002_S2_R1_001: value too great for base (error token is "0002_S2_R1_001")
Sep 05 20:52:49 ..... finished successfully
/home/zhou/t12b/RNA_seq/code/star.ht.sh: line 78: 20173-0001_S1_R1_001: value too great for base (error token is "0001_S1_R1_001")

Could you please help me to check this error? Best, JG

[alexdobin]

Hi JG,

it seems like two STAR jobs were run simultaneously, which is usually not a good idea. This means that your script called STAR twice.

Cheers Alex

[JianGuoZhou3]

Hi JG,

it seems like two STAR jobs were run simultaneously, which is usually not a good idea. This means that your script called STAR twice.

Cheers Alex

Hi Alex, thanks for your quick reply. So, you suggest just run star by one-by-one? but actually, for other paired-end RNAseq cohorts this script was worked. This error is from single-end mRNA RNA-seq. (QuantSeq 3' mRNA-Seq Library Prep Kit FWD) https://www.lexogen.com/quantseq-data-analysis/ JG

[alexdobin]

Hi JG,

running it one by one is less cumbersome. When you run 2 jobs simultaneously, they will use 2x RAM, and you need to make sure you run them from separate work directories.

Cheers Alex