Open elena-bio opened 2 months ago
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:
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.
Check out this sample user guide on how to use different stages of PBHoney.
Depends on #3 & #4