featurecounts not working on mirbase annotation file

Question

[demoraesdiogo2017]

Hello I am trying to analyze miRNA-seq data but I am having problems with the mapping. I always get pretty much 0 counts with the built in annotation file, so I got one from miRBase. However, I always get an error when I use it, it doesn't even run. I thought the error could have been in the structure of the file, so I downloaded one from GENCODEand compared both structures. They didn't seem different, but the one from GENCODE runs just like the built-in one (runs but gives zero counts). So I have no idea what is going on.

Here are the gff3 structures:

miRBase:

chr1    .   miRNA_primary_transcript    12425986    12426106    .   +   .   ID=MI0021869;Alias=MI0021869;Name=mmu-mir-6341          
chr1    .   miRNA   12426016    12426038    .   +   .   ID=MIMAT0025084;Alias=MIMAT0025084;Name=mmu-miR-6341;Derives_from=MI0021869         
chr1    .   miRNA_primary_transcript    20679010    20679082    .   +   .   ID=MI0000249;Alias=MI0000249;Name=mmu-mir-206           
chr1    .   miRNA   20679017    20679039    .   +   .   ID=MIMAT0017004;Alias=MIMAT0017004;Name=mmu-miR-206-5p;Derives_from=MI0000249           

GENCODE:

chr1    HAVANA  gene    3073253 3074322 .   +   .   ID=ENSMUSG00000102693.1;gene_id=ENSMUSG00000102693.1;gene_type=TEC;gene_status=KNOWN;gene_name=4933401J01Rik;level=2;havana_gene=OTTMUSG00000049935.1           
chr1    HAVANA  transcript  3073253 3074322 .   +   .   ID=ENSMUST00000193812.1;Parent=ENSMUSG00000102693.1;gene_id=ENSMUSG00000102693.1;transcript_id=ENSMUST00000193812.1;gene_type=TEC;gene_status=KNOWN;gene_name=4933401J01Rik;transcript_type=TEC;transcript_status=KNOWN;transcript_name=4933401J01Rik-001;level=2;transcript_support_level=NA;tag=basic;havana_gene=OTTMUSG00000049935.1;havana_transcript=OTTMUST00000127109.1         
chr1    HAVANA  exon    3073253 3074322 .   +   .   ID=exon:ENSMUST00000193812.1:1;Parent=ENSMUST00000193812.1;gene_id=ENSMUSG00000102693.1;transcript_id=ENSMUST00000193812.1;gene_type=TEC;gene_status=KNOWN;gene_name=4933401J01Rik;transcript_type=TEC;transcript_status=KNOWN;transcript_name=4933401J01Rik-001;exon_number=1;exon_id=ENSMUSE00001343744.1;level=2;transcript_support_level=NA;tag=basic;havana_gene=OTTMUSG00000049935.1;havana_transcript=OTTMUST00000127109.1           
chr1    ENSEMBL gene    3102016 3102125 .   +   .   ID=ENSMUSG00000064842.1;gene_id=ENSMUSG00000064842.1;gene_type=snRNA;gene_status=KNOWN;gene_name=Gm26206;level=3            
chr1    ENSEMBL transcript  3102016 3102125 .   +   .   ID=ENSMUST00000082908.1;Parent=ENSMUSG00000064842.1;gene_id=ENSMUSG00000064842.1;transcript_id=ENSMUST00000082908.1;gene_type=snRNA;gene_status=KNOWN;gene_name=Gm26206;transcript_type=snRNA;transcript_status=KNOWN;transcript_name=Gm26206-201;level=3;transcript_support_level=NA;tag=basic         

any idea of what could be wrong?

[GenoMax]

What does your featureCounts command line look like?

[demoraesdiogo2017]

on the one that works. I change nothing when I use the one from mirBASE.

export FC_PATH=$(command -v featureCounts | sed 's@/bin/featureCounts$@@') &&  featureCounts  -a ${FC_PATH}/annotation/mm10_RefSeq_exon.txt -F "SAF"  -o "output" -T ${GALAXY_SLOTS:-2}  -s  0  -Q  0               --minOverlap  1 --fracOverlap 0 --fracOverlapFeature 0     '/data/dnb08/galaxy_db/files/1/2/6/dataset_12675960-3c58-4a48-aba6-f4ca750e7eff.dat'  && grep -v "^#" "output" | sed -e 's|/data/dnb08/galaxy_db/files/1/2/6/dataset_12675960-3c58-4a48-aba6-f4ca750e7eff.dat|HISAT2 on data 384: aligned reads (BAM)|g' > body.txt && cut -f 1,7 body.txt > '/data/jwd02f/main/060/487/60487873/outputs/galaxy_dataset_39d1a976-03e0-48b6-9aab-2dfcee0947d6.dat'    && sed -e 's|/data/dnb08/galaxy_db/files/1/2/6/dataset_12675960-3c58-4a48-aba6-f4ca750e7eff.dat|HISAT2 on data 384: aligned reads (BAM)|g' 'output.summary' > '/data/jwd02f/main/060/487/60487873/outputs/galaxy_dataset_199b296d-de69-44ef-82a6-3866f9fa65ee.dat'