FastGA: Call to FAtoGDB failed, segmentation fault

[finn314]

Hello! I recently tried a new Cactus run on 3.3.0, but encountered segmentation faults during FastGA for several different pairwise alignments that mirrored the following:

Log from job "kind-run_fastga/instance-lq4hfery" follows:
=========>
[2026-08-19T21:46:56-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG---
[2026-08-19T21:46:56-0400] [MainThread] [I] [toil] Running Toil version 9.5.0-855577413b6e3ceb33a90b3ec415e7a3fc0badba on host c5b2.
[2026-08-19T21:46:56-0400] [MainThread] [I] [toil.worker] Working on job 'run_fastga' kind-run_fastga/instance-lq4hfery v1
[2026-08-19T21:47:34-0400] [MainThread] [I] [toil.worker] Loaded body Job('run_fastga' kind-run_fastga/instance-lq4hfery v1) from description 'run_fastga' kind-run_fastga/instance-lq4hfery v1
[2026-08-19T21:48:04-0400] [MainThread] [I] [cactus.shared.common] Running the command ['FastGA', '-pafs', '-M', '-P./fgatmp', '-T8', 'stickleback_0.f.fa', 'humpbackpufferfish_0.f.fa']
[2026-08-19T21:48:04-0400] [MainThread] [I] [toil-rt] 2026-08-19 21:48:04.670867: Running the command: "FastGA -pafs -M -P./fgatmp -T8 stickleback_0.f.fa humpbackpufferfish_0.f.fa"
[2026-08-19T21:48:10-0400] [MainThread] [W] [toil.fileStores.abstractFileStore] Failed job accessed files:
[2026-08-19T21:48:10-0400] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'job-files/kind-make_chunked_alignments/instance-ywdonmof/cleanup/file-60627c274e3445a3a01ecec1f710701e/0.fa' to path [my path]/WrkDir/toilwf-7b6f7c842e9c548a8b32629526a7fb37/ae55/job/tmp_64x_ds9/humpbackpufferfish_0.fa'
[2026-08-19T21:48:10-0400] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'job-files/kind-make_chunked_alignments/instance-ywdonmof/cleanup/file-5eb3036e77114b28a518d2d5e53fd867/0.fa' to path [my path]/WrkDir/toilwf-7b6f7c842e9c548a8b32629526a7fb37/ae55/job/tmp_64x_ds9/stickleback_0.fa'
[2026-08-19T21:48:10-0400] [MainThread] [C] [toil.worker] Worker crashed with traceback:
Traceback (most recent call last):
File "[my path]/cactus3/cactus-bin-v3.3.0/venv-cactus-v3.3.0/lib/python3.10/site-packages/toil/worker.py", line 591, in workerScript
job._runner(
File "[my path]/cactus3/cactus-bin-v3.3.0/venv-cactus-v3.3.0/lib/python3.10/site-packages/toil/job.py", line 3404, in _runner
returnValues = self._run(jobGraph=None, fileStore=fileStore)
File "[my path]/cactus3/cactus-bin-v3.3.0/venv-cactus-v3.3.0/lib/python3.10/site-packages/toil/job.py", line 3254, in _run
return self.run(fileStore)
File "[my path]/cactus3/cactus-bin-v3.3.0/venv-cactus-v3.3.0/lib/python3.10/site-packages/toil/job.py", line 3604, in run
rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs)
File "[my path]/cactus3/cactus-bin-v3.3.0/venv-cactus-v3.3.0/lib/python3.10/site-packages/cactus/paf/local_alignment.py", line 165, in run_fastga
cactus_call(parameters=fastga_cmd, outfile=alignment_file, job_memory=job.memory, work_dir=work_dir)
File "[my path]/cactus3/cactus-bin-v3.3.0/venv-cactus-v3.3.0/lib/python3.10/site-packages/cactus/shared/common.py", line 1060, 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" FastGA -pafs -M -P./fgatmp -T8 stickleback_0.f.fa humpbackpufferfish_0.f.fa exited 1: stderr=Segmentation fault (core dumped)

FastGA: Call to FAtoGDB failed
Command exited with non-zero status 1
CACTUS-LOGGED-MEMORY-IN-KB: 108852

Any advice on how to proceed?

[glennhickey]

It seems everytime I update the FastGA version in Cactus something breaks. Your best bet is to probably downgrade FastGA (making sure the -M option is set accordingly in the config).

But ideally, you'd reproduce your error on the command line and make an issue on the FastGA github (they're usually pretty fast) including links to the input data.