Using STAR to map fastq files: EXITING: because of fatal INPUT ERROR: number of input files for mate3=1 is not equal to that for mate1=3

Question

[merfer0206]

Hey there, I am trying to map my fastq genome files using STAR. However, when I enter in my code, I get this:

EXITING: because of fatal INPUT ERROR: number of input files for mate3=1 is not equal to that for mate1=3 Make sure that the number of files in --readFilesIn is the same for both mates

Anybody have any clue on how to fix this? I believe I am annotating my read1/2 and samples correctly? Also, would anyone know how to set a directory for STAR so it finds my fastq files so I dont have to keep retyping it?

many thanks!

STAR --runThreadN 4 --genomeDir /genome_index --readFilesIn Users/mfaleeva/Desktop/Day30R1/ Day-30-R1_S1_L008_R1_001.fastq,Users/mfaleeva/Desktop/Day30R2/ Day-30-R2_S2_L008_R1_001.fastq,Users/mfaleeva/Desktop/Day30R3/ Day-30-R3_S3_L008_R1_001.fastq Users/mfaleeva/Desktop/Day30R1/ Day-30-R1_S1_L008_R2_001.fastq,Users/mfaleeva/Desktop/Day30R2/ Day-30-R2_S1_L008_R2_001.fastq,Users/mfaleeva/Desktop/Day30R3/ Day-30-R3_S1_L008_R2_001.fastq--outSAMattrRGline ID:Day30_R1 , ID:Day30_R2 , ID:Day30_R3

[Ram]

Your command has a bunch of errors - which are probably copy-paste errors as no command would even start execution with as many typos. Check it thoroughly, please. There are spaces where there should be none and there are no spaces where they absolutely should be there.

[merfer0206]

such as? although rechecking I cannot see anything?

[Ram]

--readFilesIn Users/mfaleeva/Desktop/Day30R1/ Day-30-R1_S1_L008_R1_001.fastq,Users/mfaleeva/Desktop/Day30R2/ Day-30-R2_S2_L008_R1_001.fastq,Users/mfa...
-------------^-------------------------------^-------------------------------^------------------------------^

See the space between R1/ and Day-30-R1? Also the lack of / before Users? That's two huge problems. Plus, further down, you can see there's no space before --outSAMattrRGline. In addition to antonio's points on how you should be using STAR, these errors in how any command needs to be written are pretty crippling, which is why I'm guessing they're copy paste errors and not actually errors in the command you ran.

[antonioggsousa]

If you want to provide a list of SE fastq files you need to provide this list separated by comma and not space, such as:

--readFilesIn file_1.fastq,file_2.fastq,file_3.fastq

If you have PE fastq give two lists separated by comma and for the forward and reverse fastq files with a space between them:

--readFilesIn file_1_R1.fastq,file_2_R1.fastq,file_3_R1.fastq file_1_R2.fastq,file_2_R2.fastq,file_3_R2.fastq

Read this in manual - page 8

[merfer0206]

Correct me if I'm wrong, but I am doing just that? if I have 3 samples, (Day-30-R1, R2, R3), with two reads each?

STAR --runThreadN 4 --genomeDir /Users/mfaleeva/Desktop/Day30 --readFilesIn Day-30-R1_S1_L008_R1_001.fastq,Day-30-R2_S2_L008_R1_001.fastq,Day-30-R3_S3_L008_R1_001.fastq Day-30-R1_S1_L008_R2_001.fastq,Day-30-R2_S1_L008_R2_001.fastq,Day-30-R3_S1_L008_R2_001.fastq--outSAMattrRGline ID:Day30_R1 , ID:Day30_R2 , ID:Day30_R3

[antonioggsousa]

Now it looks Ok with the exception of a lack of space between Day-30-R3_S1_L008_R2_001.fastq--outSAMattrRGline the fastq sample and the parameter.

After these corrections, are you still getting the same error?

[merfer0206]

Unfortunately now the error has changed, it has stopped recognising sample3 read 1, but I guess the original error is fixed

[antonioggsousa]

Make sure that the file name is correct as well as the path.

[Ram]

Yes, that's what you're doing, although the command is incredibly difficult to read.