Stringtie Error: Getting the input alignment file is not sorted! even though file is sorted
Hi,
I am getting the following error when I try to use the Stringtie merge function:
stringtie --merge -p $threads -G DM_1-3_516_R44_potato.v6.1.working_models.gff3 -o stringtie_merged.gtf mergelist.txt
Error: the input alignment file is not sorted!
Alignments (7) already found for scaffold_128 !
As mentioned in previous posts I checked the indexed bam files and they look fine. Please see below.
samtools view -H PVX_2d_1.bam | grep "HD"
Output:
@HD VN:1.0 SO:coordinate
I checked the mergelist.txt and there are no empty spaces nor empty lines. There I have twelve samples. Before merge step I assembled transcripts using indexed bam files:
stringtie --rf -p $threads -G DM_1-3_516_R44_potato.v6.1.working_models.gff3 -o ${SAMPLE}.gtf -l ${SAMPLE} ${SAMPLE}.bam
Can someone help me in this regard? Thanks in advance.
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what is the output of a new indexing ?
I ran
samtools index PVX_2d_1.bamfollowed bysamtools view -H PVX_2d_1.bam | grep "HD"and got the following (same as earlier)Hope I didn't misunderstand what you asked me to do.
yes, that's what I wanted.