I have a fastq file from ENA that has combined R1 and R2 into same file. I need to separate them. I've done it the way it says to on BBMap but this keeps happing. I've tried redownloading, tried the fastq.gz then unzipping. I don't know what to do.
(base) -bash-4.2$ head SRR10870267.fastq
@SRR10870267.1 NB500947:631:HV5VGBGX7:1:11101:7183:1061/3
GATACACTCTAGAAGAATGGATCGANAGTAAAAGCCCCCACACCTTCATCTGCAGTGG
+
//AA/6///<//6////<///////#</6//6/<6//A////E///<//<</A/EE//
@SRR10870267.2 NB500947:631:HV5VGBGX7:1:11101:16909:1061/3
GATCATCCAGGATTCAGAATACTAANAAAGATCAGTCTCCATGTCAGATGGTATCTAT
+
//AA/<<A/6//</A//////AE6/#<////////<<<A//</E////EAEA/EA/E<
@SRR10870267.3 NB500947:631:HV5VGBGX7:1:11101:7843:1062/3
CCACAGACACATCAAAGAATGAGTAACTCAACAAAGAATACGACTGTTACCTGTAAAG
(base) -bash-4.2$ mv SRR10870267.fastq SRR10870267_S1_L001_R1_001.fastq
(base) -bash-4.2$ mv SRR10870268.fastq SRR10870268_S1_L001_R1_001.fastq
(base) -bash-4.2$ ls
LoopSTARAlign.srun Project3.log SRR10870267_S1_L001_R1_001.fastq STARAlign.srun cellranger-6.0.1 decompress.srun irradiated noinjuryp3.srun refdata-gex-GRCh38-2020-A sample_script.srun
Project1_Output RMATS.srun SRR10870268_S1_L001_R1_001.fastq STARTestRun_Output decompress.log filtered_feature_bc_matrix miniconda3 normal refdata-gex-mm10-2020-A
(base) -bash-4.2$ sbatch noinjuryp3.srun
Submitted batch job 2872249
(base) -bash-4.2$ less Project3.log
(base) -bash-4.2$ reformat.sh in = SRR10870268_S1_L001_R1_001.fastq out1 = SRR10870268_S1_L001_R1_001.fastq out2 = SRR10870268_S1_L001_R2_001.fastq
java -ea -Xmx200m -cp /network/rit/lab/bioinformaticslab/BGonzalez/miniconda3/opt/bbmap-38.22-0/current/ jgi.ReformatReads in = SRR10870268_S1_L001_R1_001.fastq out1 = SRR10870268_S1_L001_R1_001.fastq out2 = SRR10870268_S1_L001_R2_001.fastq
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 0
at shared.PreParser.<init>(PreParser.java:71)
at shared.PreParser.<init>(PreParser.java:30)
at jgi.ReformatReads.<init>(ReformatReads.java:55)
at jgi.ReformatReads.main(ReformatReads.java:45)
(base) -bash-4.2$
•
written
by
gonzalezb549 •
2 answers
You are using the same name SRR10870268_S1_L001_R1_001.fastq as your in and out1 parameters. Basically, you are overwriting the file from which you are reading.
Correct command in this case should be
reformat.sh in=SRR10870268.fastq out1=SRR10870268_R1.fastq out2=SRR10870268_R2.fastq
assuming the initial file does have interleaved reads. That would be rather unusual.
EDIT: I checked the SRA accession. This is a 10x dataset so if you need to retrieve the fastq files then you are likely best off using SRA submission. Submitters have not provided the original BAM file so you will either need to check what is in the file you can download for free or pay to download the original R1,R2,I1 files that are available via cloud SRA.
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