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