Could not resolve to contig ID

[Xieeeee]

Hi,
Thanks for providing this tool and the exciting CUT&TAG-pro. When I try to run the example, it will raises an error 'thread 'main' panicked at 'Could not resolve to contig ID', src/fragment.rs:32:23'. The issue is gone when running chr1 only (via --onlyone). I thought it fails to convert chromosome name to id, but I am not sure how to handle that.

The completed log message is ⬇️

2021-10-13T16:29:51.946Z INFO carina::file > Found File w/ tag "model" at "/home/scChromHMM/example1/model_2.txt"
2021-10-13T16:29:51.947Z INFO schrom::hmm > Read HMM model paramers: Found { #states: 2, #assays: 3 }
2021-10-13T16:29:51.947Z INFO carina::file > Found File w/ tag "common_cells" at "/home/scChromHMM/example1/cells.txt"
2021-10-13T16:29:51.952Z INFO schrom::hmm > Found 7201 cells in common assay, first cell=E2L1:AAACGCTGTAACCAGG
2021-10-13T16:29:51.955Z INFO carina::file > Found File(s) w/ tag "anchors" at ["/home/scChromHMM/example1/k27ac.txt", "/home/scChromHMM/example1/k27me3.txt", "/home/scChromHMM/example1/k4me1.txt"]
2021-10-13T16:29:51.983Z INFO schrom::hmm > Found 3 assays with [19, 22, 32] cells and [2465, 3706, 3699] anchors
2021-10-13T16:29:51.984Z INFO carina::file > Found File(s) w/ tag "fragments" at ["/home/scChromHMM/example1/h3k27ac_fragments.tsv.gz", "/home/scChromHMM/example1/h3k27me3_fragments.tsv.gz", "/home/scChromHMM/example1/h3k4me1_fragments.tsv.gz"]
2021-10-13T16:29:52.008Z INFO schrom::hmm > Found total 22 chromosomes
2021-10-13T16:29:52.008Z INFO schrom::hmm > Starting forward backward
thread 'main' panicked at 'Could not resolve to contig ID', src/fragment.rs:32:23

Thanks for any suggestions!

[Xieeeee]

Hi,
Following up to see whether I can get some suggestions, thanks!

[k3yavi]

Hi @Xieeeee ,

Thanks for reaching out, your intuition is correct that it's failing to convert chromosome name to id, reason being, the tools is designed by default to work with all 22 chromosomes and when run with the test data it fails since test data has fragments from only chromosome 1. We added the flag --onlyone to inform the tool to perform segmentation on chromosome 1 only and that's why you don't see error when you run the tool with --onlyone flag. Hope it helps.

[Xieeeee]

Hi @k3yavi ,
Really appreciate your answer. I will try running on my toy data soon and will let you know how it goes.
Cheers