Error while creating arrow files with no specific (informative) error message

[drowsygoat]

Hello!

I'm having issues with creating arrow files and the log file is not particularly informative in this case. It breaks at:

2024-11-12 13:05:55 : (ID4 : 1 of 1) Computing TSS Enrichment Scores, 7.567 mins elapsed.

2024-11-12 13:05:55 : createArrowFiles has encountered an error, checking if any ArrowFiles completed..

Full log file attached. I am using a custom genome forged with BSgenomeForge package. I tried switching to single thread operation, and enabling HDF locking, but to no avail. I am using dev (v.1.0.3).

There is no problem with the tutorial data using identical config.

There are some warnings generated that are probably NOT related to the error, but just mentioning them in case I'm wrong:

Warning messages: 1: In sprintf("%s Reading TabixFile %s Percent", prefix, ... : one argument not used by format '%s Reading TabixFile %s Percent'

Any help in how to troubleshot will be highly appreciated.

ArchR-ID4_create_arrows-3dc604761c4d50-Date-2024-11-12_Time-12-58-21.log

[rcorces]

Hi @drowsygoat! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other
responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire
a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know!
In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15.
Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.

[immanuelazn]

Hi drowsygoat, that area of code does not provide logging for the arrowfiles that have failed, so I understand your frustation.

From what I see though, you're failing during the call for Computing TSS Enrichment scores. Unfortunately I can't really help with this unless I have a reproducible example on my end. What you can do to troubleshoot a little bit more is put a browser() tag right before TSSOut <- do.call(.fastTSSEnrichment, TSSParams) is called in CreateArrow.R. In single threaded mode, you should be able to see exactly which line you get a fail in.

Best,

Immanuel

[drowsygoat]

Thanks @immanuelazn. I will try to implement your debugging suggestion. Meanwhile, I can provide R objects that I use as geneAnnotation and genomeAnnotation, as well as the fragment tsv file. Would that suffice as a reproducible example and would you have time to look at it? I understand it would be time-consuming, so just let me know, if you are willing to look at it; I will then upload the said data to the dropbox.

[immanuelazn]

Doesnt hurt, although I cannot guarantee the timeline for debugging! Feel free to share your dataset and pertinent scripts at iabdi@stanford.edu