[E::idx_find_and_load] Could not retrieve index file for 'xxxxxsorted.bam'

Question

[jenyfer]

when using htseq-count -r pos -f bam. it gves this error,but lt still run ,and give the counts,

but i did use samtools to sort the ban file samtools sort /mnt/d/RNA-SEQ/SRR13532541/SRR13532541.bam -o /mnt/d/RNA-SEQ/SRR13532541/SRR13532541sorted.bam please suggest

Answer 1

[ATpoint]

Index it: samtools index your.bam

[jenyfer]

thanks but it still gives the same error [E::idx_find_and_load] Could not retrieve index file for '/mnt/d/RNA-SEQ/SRR13532540/SRR13532540sorted.bam' 100000 GFF lines processed.and continue to process. and i have just samools my bam file and get the bai file.

OK EHHHH.thanks [E::idx_find_and_load] problem solved。however，a new warning emerging as Warning: Mate records missing for 271194 records; first such record: <SAM_Alignment object: Paired-end read 'SRR13532541.sra.16922818' aligned to chr1:[14722,14823)/+>. 22700000 alignment record pairs processed. 22800000 alignment record pairs processed. 22888742 alignment pairs processed. can u advise？