Truncated record error

[prithikasritharan]

Hi,

I am very keen on using dreams to carry out variant calling on my breast cancer samples sequenced using personalised panels. However, I am having issues running the get_training_data step as it produces an error. I am running the following code:

training_data = get_training_data(
  bam_paths = sample.bam,
  reference_path = "Homo_sapiens_assembly38.fasta",
  verbose=T)

This produces the following error:

Error in `mutate()`:
ℹ In argument: `context11 = get_reference_seq(...)`.
Caused by error in `value[[3L]]()`:
!  record 652864 (chrUn_JTFH01000093v1_decoy:3671-3681) was truncated
  file: Homo_sapiens_assembly38.fasta
Run `rlang::last_trace()` to see where the error occurred.
> rlang::last_trace()
<error/dplyr:::mutate_error>
Error in `mutate()`:
ℹ In argument: `context11 = get_reference_seq(...)`.
Caused by error in `value[[3L]]()`:
!  record 652864 (chrUn_JTFH01000093v1_decoy:3671-3681) was truncated
  file: Homo_sapiens_assembly38.fasta
---
Backtrace:
     ▆
  1. ├─dreams::get_training_data(...)
  2. │ └─dreams:::get_training_data_from_bam(...)
  3. │   └─dreams:::extract_features_from_bam(...)
  4. │     └─... %>% ...
  5. ├─dplyr::mutate(...)
  6. ├─dplyr:::mutate.data.frame(...)
  7. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
  8. │   ├─base::withCallingHandlers(...)
  9. │   └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
 10. │     └─mask$eval_all_mutate(quo)
 11. │       └─dplyr (local) eval()
 12. └─dreams:::get_reference_seq(...)
 13.   ├─Biostrings::getSeq(...)
 14.   └─Rsamtools::getSeq(...)
 15.     └─Rsamtools (local) .local(x, ...)
 16.       ├─Rsamtools::scanFa(x, param, ...)
 17.       └─Rsamtools::scanFa(x, param, ...)
 18.         └─base::tryCatch(...)
 19.           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 20.             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 21.               └─value[[3L]](cond)
 22.                 └─base::stop(conditionMessage(err), "\n  file: ", path(file))

I checked the record in the reference fasta file but couldn't find an issue and I have tried running the command with different reference fasta files but it always produces the record truncated error. I am using R v4.1.2 and dreams v0.0.0.9000. Please would you be able to help me figure out what may be causing this error?

Many thanks!!

Prithika