error while running cactus-graphmap-join

[namitadube]

Hi,
I am running the final step of pangenome using command cactus-graphmap-join but i am getting error in clip-vg. when i am running with cactus-pangenome i am getting the same issue of clip-vg. could you guide me through how to correct it. Below is the error :

[2026-06-03T11:15:38+0530] [MainThread] [C] [toil.worker] Worker crashed with traceback:
Traceback (most recent call last):
File "/opt/miniconda3/envs/cactus_env/lib/python3.13/site-packages/toil/worker.py", line 591, in workerScript
job._runner(
~~~~~~~~~~~^
jobGraph=None,
^^^^^^^^^^^^^^
...<2 lines>...
defer=defer,
^^^^^^^^^^^^
)
^
File "/opt/miniconda3/envs/cactus_env/lib/python3.13/site-packages/toil/job.py", line 3376, in _runner
returnValues = self._run(jobGraph=None, fileStore=fileStore)
File "/opt/miniconda3/envs/cactus_env/lib/python3.13/site-packages/toil/job.py", line 3254, in _run
return self.run(fileStore)
~~~~~~~~^^^^^^^^^^^
File "/opt/miniconda3/envs/cactus_env/lib/python3.13/site-packages/toil/job.py", line 3576, in run
rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs)
File "/opt/miniconda3/envs/cactus_env/lib/python3.13/site-packages/cactus/refmap/cactus_graphmap_join.py", line 826, in clip_vg
cactus_call(parameters=cmd, outfile=clipped_path, job_memory=job.memory)
~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda3/envs/cactus_env/lib/python3.13/site-packages/cactus/shared/common.py", line 916, in cactus_call
raise RuntimeError("{}Command {} exited {}: {}".format(sigill_msg, call, process.returncode, out))
RuntimeError: Command /usr/bin/time -f "CACTUS-LOGGED-MEMORY-IN-KB: %M" bash -c 'set -eo pipefail && clip-vg /tmp/toilwf-f6817e54fedf53999761a0d674e4b8b7/daf5/job/tmpaf8tzeeg/mungbean.vg.gfaffixed -f -e weilv_chr -d MINIGRAPH -L | vg mod -X 1024 - | vg paths -x - -n -Q weilv_chr -t 1 | vg clip -d 1 - -P weilv_chr | vg ids -s -' exited 1: stderr=[clip-vg] error: Cycle detected in reference path weilv_chr#0#CM166661.1 at node 1262211
error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph
error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph
error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathMutableHandleGraph
error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathMutableHandleGraph
CACTUS-LOGGED-MEMORY-IN-KB: 1001592

    [2026-06-03T11:15:38+0530] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host webtools.nbpgr.ernet.in

Thanks in advance
Namita

[glennhickey]

This seems to be a gfaffix issue. We changed the gfaffix version in cactus 3.2.0. If you are using an earlier version of cactus, please try again with the latest version (3.2.1). If you are using the latest version, you might consider trying 3.1.4 to see if rolling back to the previous gfaffix helps.