EXITING: because of fatal INPUT ERROR: number of input files for mate3=1 is not equal to that for mate1=4 Make sure that the number of files in --readFilesIn is the same for both mates

[codeneeded]

STAR --runThreadN 8 \ --genomeDir /Users/plab/Desktop/Fasta_scRNAseq/STAR_Genome_Indices/Intact/ \ --readFilesIn CP18S_L001_R2.fastq,CP18S_L002_R2.fastq,CP18S_L003_R2.fastq,CP18S_L004_R2.fastq CP18S_L001_R1.fastq,CP18S_L002_R1.fastq,CP18S_L003_R1.fastq,CP18S_L004_R1.fastq \ —-readFilesPrefix /Users/plab/Desktop/Fasta_scRNAseq/GEX_ONLY/CP18S-GEX/ \ --outFileNamePrefix /Users/plab/Desktop/Fasta_scRNAseq/CP18S_Alligned/ \ --outSAMtype BAM SortedByCoordinate

On running this I get the following error: EXITING: because of fatal INPUT ERROR: number of input files for mate3=1 is not equal to that for mate1=4 Make sure that the number of files in --readFilesIn is the same for both mates

Log File Output Below

`STAR version=2.7.10b STAR compilation time,server,dir= :/Users/distiller/project/STARcompile/source STAR git: On branch master ; commit c6f8efc2c7043ef83bf8b0d9bed36bbb6b9b1133 ; diff files:

Command Line:

STAR --runThreadN 8 --genomeDir /Users/plab/Desktop/Fasta_scRNAseq/STAR_Genome_Indices/Intact/ --readFilesIn CP18S_L001_R2.fastq,CP18S_L002_R2.fastq,CP18S_L003_R2.fastq,CP18S_L004_R2.fastq CP18S_L001_R1.fastq,CP18S_L002_R1.fastq,CP18S_L003_R1.fastq,CP18S_L004_R1.fastq —-readFilesPrefix /Users/plab/Desktop/Fasta_scRNAseq/GEX_ONLY/CP18S-GEX/ --outFileNamePrefix /Users/plab/Desktop/Fasta_scRNAseq/CP18S_Alligned/ --outSAMtype BAM SortedByCoordinate

Initial USER parameters from Command Line:

outFileNamePrefix /Users/plab/Desktop/Fasta_scRNAseq/CP18S_Alligned/

All USER parameters from Command Line:

runThreadN 8 ~RE-DEFINED genomeDir /Users/plab/Desktop/Fasta_scRNAseq/STAR_Genome_Indices/Intact/ ~RE-DEFINED readFilesIn CP18S_L001_R2.fastq,CP18S_L002_R2.fastq,CP18S_L003_R2.fastq,CP18S_L004_R2.fastq CP18S_L001_R1.fastq,CP18S_L002_R1.fastq,CP18S_L003_R1.fastq,CP18S_L004_R1.fastq —-readFilesPrefix /Users/plab/Desktop/Fasta_scRNAseq/GEX_ONLY/CP18S-GEX/ ~RE-DEFINED outFileNamePrefix /Users/plab/Desktop/Fasta_scRNAseq/CP18S_Alligned/ ~RE-DEFINED outSAMtype BAM SortedByCoordinate ~RE-DEFINED

Finished reading parameters from all sources

Final user re-defined parameters-----------------:

runThreadN 8 genomeDir /Users/plab/Desktop/Fasta_scRNAseq/STAR_Genome_Indices/Intact/ readFilesIn CP18S_L001_R2.fastq,CP18S_L002_R2.fastq,CP18S_L003_R2.fastq,CP18S_L004_R2.fastq CP18S_L001_R1.fastq,CP18S_L002_R1.fastq,CP18S_L003_R1.fastq,CP18S_L004_R1.fastq —-readFilesPrefix /Users/plab/Desktop/Fasta_scRNAseq/GEX_ONLY/CP18S-GEX/
outFileNamePrefix /Users/plab/Desktop/Fasta_scRNAseq/CP18S_Alligned/ outSAMtype BAM SortedByCoordinate

---

Final effective command line:

STAR --runThreadN 8 --genomeDir /Users/plab/Desktop/Fasta_scRNAseq/STAR_Genome_Indices/Intact/ --readFilesIn CP18S_L001_R2.fastq,CP18S_L002_R2.fastq,CP18S_L003_R2.fastq,CP18S_L004_R2.fastq CP18S_L001_R1.fastq,CP18S_L002_R1.fastq,CP18S_L003_R1.fastq,CP18S_L004_R1.fastq —-readFilesPrefix /Users/plab/Desktop/Fasta_scRNAseq/GEX_ONLY/CP18S-GEX/ --outFileNamePrefix /Users/plab/Desktop/Fasta_scRNAseq/CP18S_Alligned/ --outSAMtype BAM SortedByCoordinate

EXITING: because of fatal INPUT ERROR: number of input files for mate3=1 is not equal to that for mate1=4 Make sure that the number of files in --readFilesIn is the same for both mates

Aug 18 11:28:56 ...... FATAL ERROR, exiting `

This was run on Mac OS Ventura

[alexdobin]

The dash in —-readFilesPrefix looks wrong.

[codeneeded]

It seems to be working now. Thank you so much!

[codeneeded]

Am I supposed to put the R2 Files or the R1 files first? (This is from 10x genomics, single cell output)

[alexdobin]

For 10X data you need to use --solo* options (see https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md), and specify --readFilesIn R2 R1.