I am running the htseq-count but get the [E::idx_find_and_load] warning. The bam files were sorted with name but without index. It is not required for index when running htseq-count, correct?
*CODE:
htseq-count -f bam \ -s no \ -t exon \ -m union \ -i gene_id \ $sample \ $gtf > $out/${file%.sorted.query.bam}.counts.txt*
ERROR:
1400000 GFF lines processed. 1500000 GFF lines processed. 1600000 GFF lines processed. 1700000 GFF lines processed. 1800000 GFF lines processed. 1900000 GFF lines processed. 1902096 GFF lines processed. [E::idx_find_and_load] Could not retrieve index file for '/bgfs/mkoenigshoff/huqj/DataAnalysis/rna_seq/Spc_Tfam/Mapping/HISAT2/HISAT2_sort/SCTM_11_TF5579.sorted.query.bam' 100000 SAM alignment record pairs processed. 200000 SAM alignment record pairs processed. 300000 SAM alignment record pairs processed. 400000 SAM alignment record pairs processed.
Giving a look on other forums it appears that not having the index file may cause problems. I would suggest indexing the file and retrying, just to see what happens.