[main_samview] fail to read the header from "-"

[kishor2019]

Bash script:

#Set input and parameters
round=2
threads=20
read1=/mnt/disk2/Lab_Users/KISHOR/mnspt4/tenili_reseq_50x/X101SC23121795-Z01-J001/00.CleanData/3157_3/3157_3_1.clean.fq.gz
read2=/mnt/disk2/Lab_Users/KISHOR/mnspt4/tenili_reseq_50x/X101SC23121795-Z01-J001/00.CleanData/3157_3/3157_3_2.clean.fq.gz
input=/mnt/disk2/Lab_Users/KISHOR/mnspt4/assembly_annotation/NECAT/manual/tenili.fa
for ((i=1; i<=${round};i++)); do
#step 1:
#index the genome file and do alignment
bwa index ${input};
bwa mem -t ${threads} ${input} ${read1} ${read2}|samtools view --threads 3 -F 0x4 -b -|samtools fixmate -m --threads 3 - -|samtools sort -m 2g --threads 5 -|samtools markdup --threads 5 -r - sgs.sort.bam
#index bam and genome files
samtools index -@ ${threads} sgs.sort.bam;
samtools faidx ${input};
(base)[room@black01 manual]$
python /mnt/genome3/Lab_Users/Kishor/DISK_2/softwares/NextPolish/lib/nextpolish1.py -g ${input} -t 1 -p ${threads} -s sgs.sort.bam > tenili.polishtemp.fa;
input=tenili.polishtemp.fa;
#step2:
#index genome file and do alignment
bwa index ${input};
bwa mem -t ${threads} ${input} ${read1} ${read2}|samtools view --threads 3 -F 0x4 -b -|samtools fixmate -m --threads 3 - -|samtools sort -m 2g --threads 5 -|samtools markdup --threads 5 -r - sgs.sort.bam
#index bam and genome files
samtools index -@ ${threads} sgs.sort.bam;
samtools faidx ${input};
#polish genome file
pythonn /mnt/genome3/Lab_Users/Kishor/DISK_2/softwares/NextPolish/lib/nextpolish1.py -g ${input} -t 2 -p ${threads} -s sgs.sort.bam > tenili.nextpolish.fa;
input=tenili.nextpolish.fa;
done;
#Finally polished genome file: tenili.nextpolish.fa

Error text:

[main_samview] fail to read the header from "-".
[bam_mating_core] ERROR: Couldn't read header
samtools sort: failed to read header from "-"
[markdup] error reading header
samtools index: "sgs.sort.bam" is in a format that cannot be usefully indexed
[faidx] Could not build fai index tenili.polishtemp.fa.fai

Can i have please have any help to solve this issue?

[moold]

I think you can try to update samtools to the lastest version.