EXITING: because of fatal INPUT file error: could not open read file
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6 months 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
STAR genome mapping fastq • 755 views
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Can you anyway do ls -l of those files where you execute the STAR command and post the output of that command here? thx

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(base) Marias-MBP:genome_index mfaleeva$ ls -l
total 8
-rw-r--r--   1 mfaleeva  staff     0 11 Jan 19:16 Aligned.out.sam
-rw-r--r--   1 mfaleeva  staff  2612 11 Jan 19:16 Log.out
-rw-r--r--   1 mfaleeva  staff     0 11 Jan 19:16 Log.progress.out
drwx------   5 mfaleeva  staff   160 11 Jan 19:16 _STARtmp
drwx------  18 mfaleeva  staff   576 10 Jan 01:12 genome_index
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If you executed STAR in 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).

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Sorry for stupid question, but if the STAR command didnt run because of the error, why would the files be there anyway?

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EXITING: because of fatal INPUT file error: could not open read file: Day-30-R3_S3_L008_R1_001.fastq.gz

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.gz or go into the directory where the data files are and then re-execute the command.

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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.

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