Giraffe stuck forever on some hifi reads on specific pangenomes

[leone93]

1. What were you trying to do?
Mapping some hifi reads sample on different pangenomes made with cactus.

2. What did you want to happen?
Going to have the proper .pack file at the end of the mapping

3. What actually happened?
Some samples that have zero problem mapping on some pangenomes, stuck forever on different ones. There is no apparent error. Just stay there forever.

4. If you got a line like Stack trace path: /somewhere/on/your/computer/stacktrace.txt, please copy-paste the contents of that file here:
Nope, because there is no apparent error from giraffe. Will just stay there forever.

5. What data and command can the vg dev team use to make the problem happen?
I can send you both one of the pangenome not working and one of the samples. Just let me know how.

6. What does running vg version say?
I tried all the last 4 version of vg from 1.66 to 1.69. On different cluster or workstation. Nothing change.
This is the last one, Bologna.

vg version v1.69.0 "Bologna"
Compiled with g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 on Linux
Linked against libstd++ 20230528
Using HTSlib headers 101990, library 1.19.1-29-g3cfe8769Place vg version output here

[leone93]

mapping and packing

        vg giraffe -Z "$DATADIR"/pangenome_2025/"$pangenome_dir"/"$pangenome".gbz \
        --parameter-preset hifi -p --sample "$sample" \
        -f "$i" -o gam -t "$thr" | \
        vg pack -x "$DATADIR"/pangenome_2025/"$pangenome_dir"/"$pangenome".gbz -Q 5 \
        -g - -o "$ALIGN_DIR"/"$sample"."$pangenome".pack -t "$thr"

[faithokamoto]

You say it's hanging on the giraffe command, right, not the pack command? Is the pack command relevant to this error?

Also, before sending along the entire graph, maybe we can debug this with log files. Can you find some specific read that causes hanging (use binary search on one of the problematic inputs) and then post the log created by aligning that read with the --show-work flag? Up until it starts repeating itself or stops or whatever.

[leone93]

I am going through binary search and I will be back to you. Thanks @faithokamoto

[leone93]

read_SE_68_07.log
read_SE_9129_05.log

Dear @faithokamoto , trough binary search I was able to identify some problematic reads. Here is an example of two hanging read log files.
Please let me know your thoughts. Thanks Leo