Hi,

I am trying to merge 3 GTFs that have assembled using stringtie --merge. I ran the following command:

/home/e0470749/stringtie/stringtie --merge -G /home/e0470749/reference_genome_ensembl/Homo_sapiens.GRCh38.99.gtf -o /gpfs/eplab/Nathaniel/HPAF2_celllines_star-stringtie/stringtie-merge/HPAFII_merged.gtf -p 4 /gpfs/eplab/Nathaniel/HPAF2_celllines_star-stringtie/stringtie/assembly_GTF_list.txt

However, I get the following error:

Error getting header ID# for gseq 1 (file: /gpfs/eplab/Nathaniel/HPAF2_celllines_star-stringtie/stringtie/H2_Veh24hr-1/H2_Veh24hr-1.gtf)

These are the first few lines of H2_Veh24hr-1.gtf:

# /home/e0470749/stringtie/stringtie H2_Veh24hr-1_Aligned.sortedByCoord.out.bam -p 12 -G /home/e0470749/reference_genome_ensembl/Homo_sapiens.GRCh38.99.gtf --rf -o /gpfs/eplab/Nathaniel/HPAF2_celllines_star-stringtie/stringtie/H2_Veh24hr-1/H2_Veh24hr-1.gtf -v -eB # StringTie version 2.1.2 1 StringTie transcript 1167104 1167198 1000 + . gene_id "ENSG00000207730"; transcript_id "ENST00000384997"; ref_gene_name "MIR200B"; cov "1.000000"; FPKM "0.164038"; TPM "0.379526"; 1 StringTie exon 1167104 1167198 1000 + . gene_id "ENSG00000207730"; transcript_id "ENST00000384997"; exon_number "1"; ref_gene_name "MIR200B"; cov "1.000000"; 1 StringTie transcript 1167863 1167952 1000 + . gene_id "ENSG00000207607"; transcript_id "ENST00000384875"; ref_gene_name "MIR200A"; cov "0.866667"; FPKM "0.142166"; TPM "0.328922";

My assembly_GTF_list.txt looks like this:

/gpfs/eplab/Nathaniel/HPAF2_celllines_star-stringtie/stringtie/H2_Veh24hr-1/H2_Veh24hr-1.gtf /gpfs/eplab/Nathaniel/HPAF2_celllines_star-stringtie/stringtie/H2_Veh24hr-2/H2_Veh24hr-2.gtf /gpfs/eplab/Nathaniel/HPAF2_celllines_star-stringtie/stringtie/H2_Veh24hr-3/H2_Veh24hr-3.gtf

I have run stringtie merge a few times before and it has always worked. Can someone help me to solve this error?