Problem running epiVIA

[benjytan88]

Hi, I have been trying to run epiVIA for my scATAC-seq data but fail to produce any results every time. And the error message I receive is:

[E::bwa_idx_load_from_disk] fail to locate the index files
Start Parsing Bam
Finish Parsing Bam 8584.236718654633
Finish ChimericPair 8589.17962384224
Traceback (most recent call last):
  File "/home/data/bt/anaconda3/envs/epiVia/bin/epiVIA", line 8, in <module>
    sys.exit(main())
  File "/home/data/bt/anaconda3/envs/epiVia/lib/python3.7/site-packages/epiVIA/chimera.py", line 624, in main
    ReAlignment(fapath, args.HostIndex, chimera_fragments, vector_reads)
  File "/home/data/bt/anaconda3/envs/epiVia/lib/python3.7/site-packages/epiVIA/chimera.py", line 477, in ReAlignment
    raise Exception
Exception

The command line I use to run epiVIA is:

epiVIA --Provirus ./epiVIA_ref/NL43_virus.fa --ltr5_start 1 --ltr5_end 636 --ltr3_start 9712 --ltr3_end 10347 --HostIndex ./epiVIA_ref/hg38/hg38 --Host2bit ./epiVIA_ref/hg38.2bit --tempdir ./temp/ ./Red/outs/atac_possorted_bam.bam ./epiVIA/Red/

Could the problem related to BWA and could you please explain what should I provide to the parameters --HostIndex and --Host2bit?

In my command above, for the --Host2bit parameter, I provided the path to the hg38.2bit file while for the --HostIndex parameter, I provided the path to the hg38 reference genome indexed with BWA.

Looking forward for your reply as I really want to get this to work... Thank you!