STAR cannot read fastq files

Question

[spela.j]

Hi, I have problem with mapping using STAR. I have downloaded fastq.gz files from SRA Explorer. When I do mapping to human genome, STAR cannot read fastq.gz files as it says that there is no read permision - EXITING: because of fatal INPUT file error: could not open read file. I checked permision and it seems fine (-rw-r--r-- 1).

Does anyone have idea how can I fix this? Thank you

[biofalconch]

Check this past issue: EXITING: because of fatal INPUT file error: could not open read file , the problem usually is having the wrong path to the reads in the command :)

[ATpoint]

Please show the command. Without that it's all speculation.

[spela.j]

~/mapping/STAR-2.7.10b/source$ ./STAR --runThreadN 16 --genomeDir /home/sjelesijevic/mapping/genomeDir --readFilesIn /home/sjelesijevic/rnaseq/SRR24900411_GSM7473896_P1371_Homo_sapiens_RNA-Seq_1.fastq.gz SRR24900411_GSM7473896_P1371_Homo_sapiens_RNA-Seq_2.fastq.gz --readFilesCommand gunzip -c --outFileNamePrefix /home/sjelesijevic/mapping/STAR_output/SRR24900411 --outSAMtype BAM Unsorted
!!!!! WARNING:  Could not ls SRR24900411_GSM7473896_P1371_Homo_sapiens_RNA-Seq_2.fastq.gz

EXITING: because of fatal INPUT file error: could not open read file: SRR24900411_GSM7473896_P1371_Homo_sapiens_RNA-Seq_2.fastq.gz
SOLUTION: check that this file exists and has read permision.

This is the command.

And I checked permision:

ls -l SRR24900411_GSM7473896_P1371_Homo_sapiens_RNA-Seq_1.fastq.gz SRR24900411_GSM7473896_P1371_Homo_sapiens_RNA-Seq_2.fastq.gz
-rw-r--r-- 1 sjelesijevic sjelesijevic 2285490762 May  6 12:20 SRR24900411_GSM7473896_P1371_Homo_sapiens_RNA-Seq_1.fastq.gz
-rw-r--r-- 1 sjelesijevic sjelesijevic  416544624 Jan  1  1970 SRR24900411_GSM7473896_P1371_Homo_sapiens_RNA-Seq_2.fastq.gz

Answer 1

[biofalconch]

Just from a quick scan seems you are missing the path on the second set of reads (the /home/sjelesijevic/rnaseq/ bit)

[spela.j]

Yes, that was it. The missing path for the second one. Thanks :)