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$