Unable to run Haptree

[vinaydeep26]

Hello I'm unable to Run Haptree for Some Reason, Please if you can reply soon that'll be great because we're working on a publication and will cite HaptreeX if it works.
I try to run the Command :
haptreex -v A_J_DBA_calls.vcf -d ../AJ_DBA_2J_sorted_using_Picard_Tools_dedup_withreadgroups_with_changed_sample_name.bam -o outputfile.txt &> log_test_hapree.txt &

but i always get an error like this:

Aborted                 (core dumped) haptreex -v A_J_DBA_calls.vcf -d ../AJ_DBA_2J_sorted_using_Picard_Tools_dedup_withreadgroups_with_changed_sample_name.bam -o outputfile.txt

ValueError: not BGZF compressed
raised from: sam_itr_next
/home/vagrant/.seq/lib/seq/stdlib/bio/c_htslib.seq:65:9

then i try to Bgzip the VCF file and tabix it using tabix -p vcf vcffile
then i get this error:

IndexError: list index out of range

raised from: _idx_check
/home/vagrant/.seq/lib/seq/stdlib/core/collections/list.seq:322:13

[vinaydeep26]

Here are the screenshots. I'm not sure what am i doing wrong can you guys help me out please?
@inumanag @LillianZ @arshajii @HarisSmajlovic

[inumanag]

Can you please decompress VCF (via gunzip) and then see if it works with the uncompressed VCF?

[vinaydeep26]

@inumanag In the first run i'm running with a decompressed file, then i compressed it and it started showing me the index error

[vinaydeep26]

@inumanag @LillianZ

[pdimens]

@inumanag @LillianZ I see the same issue if using a BCF file or a bam file. It's not practical to be forced to decompress these large common datastores to perform this analysis

[pdimens]

@vinaydeep26 your issue is the sam file, I think, as the error called is raised from: sam_itr_next, suggesting it's the alignment file