Hi everyone, I am trying to do htseq-count with an in house transcriptome annotation and for some reason is just not working. I get an output with 0 for all the quantifications. Any suggestions? I am running out of ideas.... Thanks !!

samtools view file.bam | head
K00311:84:HYCNTBBXX:1:2227:13971:25034  0   TRINITY_GG_99991_c4_g1_i13.mrna1    144 1   25M *   0   0   CCAGAATTTAGAGCTTTGTCCAGAT   AAFFFJJJJJJJJJJJJJJJJJJJJ   AS:i:0  XS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:25 YT:Z:UU
K00311:84:HYCNTBBXX:2:1217:21816:46399  0   TRINITY_GG_99991_c4_g1_i13.mrna1    89  1   26M *   0   0   CAGCTCTGACTGTGAGGTGGTGGGCA  AAFFFJJJJJJJJJJJJJJJJJJJJJ  AS:i:0  XS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:26 YT:Z:UU
K00311:84:HYCNTBBXX:2:2220:23084:27813  0   TRINITY_GG_99991_c4_g1_i13.mrna1    51  1   29M *   0   0   ACTGTCGTACCTCAAGAGCCAAGGTTGGG   AAFFFJJJJJJJJJJJJJJJJJJJJJJJJ   AS:i:0  XS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:29 YT:Z:UU

head file.gff3
LQNS02276620.1  phaw_gmap_genome    CDS 17889810    17889973    98  +   0   ID=TRINITY_GG_99991_c4_g1_i13.mrna1.cds1;Name=TRINITY_GG_99991_c4_g1_i13;Parent=TRINITY_GG_99991_c4_g1_i13.mrna1;Target=TRINITY_GG_99991_c4_g1_i13 23 186 +
LQNS02276620.1  phaw_gmap_genome    CDS 17891693    17891871    99  +   2   ID=TRINITY_GG_99991_c4_g1_i13.mrna1.cds2;Name=TRINITY_GG_99991_c4_g1_i13;Parent=TRINITY_GG_99991_c4_g1_i13.mrna1;Target=TRINITY_GG_99991_c4_g1_i13 187 365 +
LQNS02276620.1  phaw_gmap_genome    CDS 17892279    17892486    100 +   1   ID=TRINITY_GG_99991_c4_g1_i13.mrna1.cds3;Name=TRINITY_GG_99991_c4_g1_i13;Parent=TRINITY_GG_99991_c4_g1_i13.mrna1;Target=TRINITY_GG_99991_c4_g1_i13 366 573 +
LQNS02276620.1  phaw_gmap_genome    CDS 17893338    17893515    98  +   2   ID=TRINITY_GG_99991_c4_g1_i13.mrna1.cds4;Name=TRINITY_GG_99991_c4_g1_i13;Parent=TRINITY_GG_99991_c4_g1_i13.mrna1;Target=TRINITY_GG_99991_c4_g1_i13 574 751 +
LQNS02276620.1  phaw_gmap_genome    CDS 17894428    17894542    100 +   0   ID=TRINITY_GG_99991_c4_g1_i13.mrna1.cds5;Name=TRINITY_GG_99991_c4_g1_i13;Parent=TRINITY_GG_99991_c4_g1_i13.mrna1;Target=TRINITY_GG_99991_c4_g1_i13 752 866 +

htseq-count -t CDS -i Parent -m union -a 0 -f bam file.bam file.gff3 > results_htseq_union_all.txt