Duplicated sequence samtools

Question

[Moinuddin]

Hi Community!!

I am running bowtie2 and samtools for read mapping. Here is my command:

 #!/bin/bash
#SBATCH --job-name="bt10"
#SBATCH --partition=Orion
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=36
#SBATCH --mem=350GB
#SBATCH --time=20-00:00:00

module load bowtie2/2.5.1
module load samtools/1.10

#Mapping 

for sample in `cat /projects/luo_lab/ncldv/trimmomatic/aloha2/sample_list_6.txt`
do
index_prefix="/projects/luo_lab/ncldv/bowtie2/index/total_al1_al2_contigs/total_al1_al2_contigs_index"
reads1="/projects/luo_lab/ncldv/trimmomatic/aloha2/${sample}_1_paired.fastq.gz"
reads2="/projects/luo_lab/ncldv/trimmomatic/aloha2/${sample}_2_paired.fastq.gz"
output_dir="/projects/luo_lab/ncldv/bowtie2/total_aloha1_aloha2"

# Run Bowtie2 for paired-end reads
bowtie2 -p 36 -x "$index_prefix" \
  -1 "$reads1" \
  -2 "$reads2" | samtools sort -o "$output_dir/${sample}_sorted.bam";done

I am having this error:

W::sam_hdr_create] Duplicated sequence 'c_000007023807_aloha2_low_cov'
[W::sam_hdr_create] Duplicated sequence 'c_000007023811_aloha2_low_cov'
[W::sam_hdr_create] Duplicated sequence 'c_000007023813_aloha2_low_cov'
[W::sam_hdr_create] Duplicated sequence 'c_000007023817_aloha2_low_cov'
[W::sam_hdr_create] Duplicated sequence 'c_000007023819_aloha2_low_cov'

What can be the probable cause of this error? Thanks in advance

[GenoMax]

Consider using SLURM job arrays if you want to use a for loop inside a single SLURM job: https://hpc.nmsu.edu/discovery/slurm/job-arrays/

Answer 1

[Pierre Lindenbaum]

the sequence c_000007023807_aloha2_low_cov is duplicated in the reference

grep c_000007023807_aloha2_low_cov  path/to/reference.fasta