error when using bambu to quantify SIRV

[yinshiyi]

Hi Bambu developer,
I use bambu without issue with host ref genome.
However, when quantify using SIRV genome gtf. I encounter the following bug.
I tested my SIRV ref and gtf pair with other tools and those run fine.
I am wondering if you have any ideas on this issue?
Thank you.

sirv_ann <- prepareAnnotations(sirv_gtf)
sirv.quantOnly <- bambu(reads = bam, annotations = sirv_ann, genome = sirv_fa, discovery = FALSE, lowMemory=FALSE)
--- Start generating read class files ---
[E::faidx_fetch_seq2] Failed to retrieve block: unexpected end of file
Error: BiocParallel errors
1 remote errors, element index: 1
0 unevaluated and other errors
first remote error:
Error in value[3L]: record 165 (SIRV12003:11991-12000) failed
file: SIRV_ERCC_longSIRV_multi-fasta_20210507.fasta
In addition: Warning messages:
1: There was 1 warning in summarise().
In argument: intersectWidth = max(intersectWidth).
Caused by warning in max():
! no non-missing arguments to max; returning -Inf
2: There was 1 warning in summarise().
In argument: intersectWidth = max(intersectWidth).
Caused by warning in max():
! no non-missing arguments to max; returning -Inf
3: There was 1 warning in summarise().
In argument: intersectWidth = max(intersectWidth).
Caused by warning in max():
! no non-missing arguments to max; returning -Inf

[yinshiyi]

I temp got around the issue by removing the entry SIRV12003 entirely.

[alexpan00]

I had the same problem, and it was fixed by adding a "\n" after the sequence of the SIRV12003.

[yinshiyi]

@alexpan00 , amazing, thank you!
I will look into why other tools ran fine, and only Bambu requires this fix.

[cying111]

Hi @yinshiyi , thanks for reporting this, yes, I think I have also encountered this and likely the root cause is the SIRV fasta file is not properly formatted, in bambu, we use FaFile: BSGenome packages, which depend heavily the proper format of fasta sequences.