Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files

Question

[Deepthi]

~/bowtie-1.3.1-linux-x86_64

This version of bowtie in HPC produces sam or bam files even with different fastq files and gives Error reading _rstarts[] array: 21720, 23124 I have pasted my code below for reference and aslo error.Thanks.

./bowtie --no-unal --threads 3 --sam ~/neural_GSE181050/indexes/GRCh38 ~/hspiRNA_13690/cut_results/adult_cbl_ERR12409218t.fastq ~/hspiRNA_13690/bam_files/adult_cbl_ERR12409218t.bam

Setting the index via positional argument will be deprecated in a future release. Please use -x option instead.

Error reading _rstarts[] array: 21720, 23124

Answer 1

[ATpoint]

bowtie -x idx file.fastq | samtools view -o out.bam

You might be messing up things with these positional arguments. Use this above. Use samtools as bowtie returns sam, not bam.

If that doesn't work then probably your fastq file is corrupted. What is file adult_cbl_ERR12409218t.fastq and head adult_cbl_ERR12409218t.fastq? Any reason it's not gzipped? No advantage in that.

[Deepthi]

Thanks will check and update here.

[ATpoint]

See me edit I just made for the fastq check.

[Deepthi]

pop up with sam error . Error reading _rstarts[] array: 21720, 23124

[Deepthi]

I unzipped the fastq files to check whether reads are trimmed adapter or not. I have checked the quality control using fastqc they are good quality. how do I know about the fastq files are corrupt?