Entering edit mode
2.2 years ago
merfer0206 • 0
When I try and map my fastq files in STAR, I get the error:
EXITING: because of fatal INPUT file error: could not open read file: Day-30-R3_S3_L008_R1_001.fastq.gz SOLUTION: check that this file exists and has read permision
However, I have checked that both the name and the directory of this file is correct, so I do not see the issue? Could anyone help out? Many thanks!
STAR --runThreadN 4 --genomeDir /Users/mfaleeva/Desktop/Day30 --readFilesCommand gunzip -c --readFilesIn Day-30-R1_S1_L008_R1_001.fastq.gz,Day-30-R2_S2_L008_R1_001.fastq.gz,Day-30-R3_S3_L008_R1_001.fastq.gz Day-30-R1_S1_L008_R2_001.fastq.gz,Day-30-R2_S2_L008_R2_001.fastq.gz,Day-30-R3_S3_L008_R2_001.fastq.gz --outSAMattrRGline ID:Day30_R1 , ID:Day30_R2 , ID:Day30_R3
Can you anyway do
ls -lof those files where you execute the STAR command and post the output of that command here? thx
If you executed
STARin this directory then there are no data files here. You need to likely be in one directory up (or where ever the data files are).
Sorry for stupid question, but if the STAR command didnt run because of the error, why would the files be there anyway?
STAR command did not run because the program was not able to open your data file as noted in the error you posted in original question. So the file name may be correct but that file is not present in the directory where you ran the command. You need to provide full/relative path to the location where that file is
/path_to/Day-30-R3_S3_L008_R1_001.fastq.gzor go into the directory where the data files are and then re-execute the command.
I think that GenoMax got the issue. To answer your questions, the generated files are mostly log files (in which you will probably find the error messages again and the command you issued). The file
Aligned.out.sam, which is the first result you should obtain, is indeed empty (see the 0 on the fifth column of your output), and it is empty because STAR could not locate the read file. Try to follow GenoMax's advice and either run star from the folder in which you have the file Day-30-R3_S3_L008_R1_001.fastq.gz or (preferred) run STAR from an empty folder but provide the full path to file name.
Hi, I'm having the exact same issue. I'm in the directory with my .fq files and I believe that my paths all point to the appropriate directory, yet I get the same error.
This is the first file in a list of 22 .fq files.
I ran ls -l and got the following
Can you post your full command line?
Is this a multiline input and single line input for fastqs? In addition, there are multiple samples and for each sample, there seem to be R1 and R2. Check if your input is correct for multiple samples and for paired reads.
It is not a question of efficiency. You need to follow directions required for specifying the files. You can't have spaces around the commas separating file names. STAR manual specifies the following:
These are single-end reads, not paired-end. And the R1, R2 etc are replicates for each treatment/ condition. I though reading them all in at once would be more efficient. Also, it’s balking at taking in the very first set of data. Maybe I’ll try just one sample and see if I can get that to work.
R1/R2 in file names have a specific meaning for paired-end Illumina data. They represent two reads from two ends of a set of fragments. STAR will expect that to be the case and I wonder if that is confusing it since you have single-end data.
If R1/R2 in names represent replicates in your case then try renaming the files so they say something like
rep1instead of R1.
Also, I removed all of the commas ',' and reran the whole script with all the replicates and I don't get the error below anymore. I think it was expecting there to be a comma at the end of the file name.
However, now I get "Segmentation fault: 11", and it doesn't run.
what's the genome size and how did you generate indices?
400MB, and I used STAR to generate the indices/suffix arrays.
Let's see. I added the comma back between each file, removed the space, and ran the code WITH the R1, R2, R3, b/c I hadn't seen this message yet.
It ran and completed.
Is it safe to assume that b/c I entered it as single-end (comma separated, no space) that my Aligned.sortedByCoord.out.bam is okay? or do I need to rerun?