Figure out if PBHoney can generate a VCF file from the inputs

[elena-bio]

Check out this sample user guide on how to use different stages of PBHoney.

Depends on #3 & #4

[elena-bio]

When trying to run pie stage of PBHoney on our first sample BAM file, we encountered the following error:

(pbhoney-env) [elehos@g-12-l0002 dna_lr_seq]$ Honey pie bam_files/pb_na24385.bwa.sorted.bam bam_files/GCA_000001405.15_GRCh38_no_alt_analysis_set_maskedGRC_exclusions.fasta

Please Cite: English, Adam C., William J. Salerno, Jeffery G.
             Reid. "PBHoney: identyfying genomic variants via
             long-read discordance and interrupted mapping."
             BMC Bioinformatics 2014, 15:180 (June 10, 2014).
             doi:10.1186/1471-2105-15-180

2024-06-16 03:39:17,515 [INFO] Running [/home/projects/cu_10160/people/elehos/dna_lr_seq/pbhoney-15.8.24/Honey](https://github.com/home/projects/cu_10160/people/elehos/dna_lr_seq/pbhoney-15.8.24/Honey) pie bam_files/pb_na24385.bwa.sorted.bam bam_files/GCA_000001405.15_GRCh38_no_alt_analysis_set_maskedGRC_exclusions.fasta
2024-06-16 03:39:17,515 [INFO] Mapping Tails
2024-06-16 03:39:17,529 [INFO] Extracting tails
Traceback (most recent call last):
  File "/home/projects/cu_10160/people/elehos/dna_lr_seq/pbhoney-15.8.24/Honey", line 51, in <module>
    parseArgs()
  File "/home/projects/cu_10160/people/elehos/dna_lr_seq/pbhoney-15.8.24/Honey", line 48, in parseArgs
    STAGES[args.stage](args.options)
  File "/home/projects/cu_10160/people/elehos/dna_lr_seq/pbhoney-15.8.24/pbsuite/honey/bampie.py", line 392, in run
    pairs.append((file, mapTails(file, args)))
  File "/home/projects/cu_10160/people/elehos/dna_lr_seq/pbhoney-15.8.24/pbsuite/honey/bampie.py", line 336, in mapTails
    r, t, m = extractTails(bam, outFq=tailfastq, minLength=args.minTail)
  File "/home/projects/cu_10160/people/elehos/dna_lr_seq/pbhoney-15.8.24/pbsuite/honey/bampie.py", line 110, in extractTails
    code, length = read.cigar[0]
IndexError: list index out of range

At this point in our investigation we can think of at least 2 different paths to move forward:

• Since PBHoney is an open source Python product, we can run it with a debugger and try to figure out if we can resolve the issue;
• Or, we can try to use different input BAM files, to see if the error above is due to bad data.

[elena-bio]

• Upon review, I have decided to address and fix the issue directly in the source code.

[elena-bio]

• I ran the code again after fixing the issue, but I got this error :Can not convert non-pacbio reads to pbbam record.

[elena-bio]

After encountering this error, my next step will involve exploring an alternative approach by using a different dataset. Initially, I encountered difficulties downloading the dataset directly to Computerome from the provided link.

As a workaround, I first downloaded the dataset to my external hard drive. Subsequently, I transferred it to Computerome using the following command:

This method allowed me to successfully transfer the dataset to Computerome for further analysis and processing.