Error while aligning with STAR

Question

[Omnia]

Hi,

When I try to run this command. Note that I change working directory to directory containing fast files

STAR --genomeDir /N/slate/ogaafer/mm10_index --runThreadN 8 \
    --readFilesIn SRR8278856_1.fastq,SRR8278856_2.fastq SRR8278857_1.fastq,SRR8278857_2.fastq SRR8278859_1.fastq,SRR8278859_2.fastq \
    --outSAMattrRGline ID:cont1 , ID:cont2 , ID:cont3 \
    --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within \
    --outSAMattributes Standard

I get this error

EXITING: because of fatal INPUT ERROR: number of input read files: 2 does not agree with number of read group RG entries: 3
Make sure that the number of RG lines in --outSAMattrRGline is equal to either 1, or the number of input read files in --readFilesIn

Answer 1

[h.mon]

From Run STAR with 4 fastq files, ERROR (and now I will plagiarize):

You are not using correct separation of the file names. Separate group of paired-end mates by a space and multiple R1/R2 files by commas. Try:

--readFilesIn SRR8278856_1.fastq,SRR8278857_1.fastq,SRR8278859_1.fastq SRR8278856_2.fastq,SRR8278857_2.fastq,SRR8278859_2.fastq