progressiveMauve exitcode 11

[LBumiller]

Hello!
I'm trying to run CanSNPer2 on multiple Francisella tularensis Assemblies, but it keeps aborting on exitcode 11 - This progressiveMauve error is showing up for bad genomes containing short repetative contigs or sequence contains dashes.

Considering it might be an issue with the present Assemblies I've tried to run it on a few NCBI one contig Sequences and a published Assembly.
However, no matter the input, I kept getting the following error:

CanSNPer2 --debug --database database/francisella_tularensis.db test_data/*.fasta --summary

2025-02-05 12:18:17,717 CanSNPerTree [DEBUG]  Namespace(query=['test_data/FSC200.fasta', 'test_data/LVS.fasta', 'test_data/OSU18.fasta', 'test_data/SAMEA2240486.contigs.fasta'], database='database/francisella_tularensis.db', outdir='results', save_tree=False, no_snpfiles=True, summary=True, refdir='references/', workdir='./', read_input=False, min_required_hits=3, strictness=0.7, keep_going=False, rerun=False, skip_mauve=False, keep_temp=False, tmpdir='/tmp/CanSNPer2', logdir='logs/', verbose=None, debug=10, supress=30, version=False)
2025-02-05 12:18:17,717 CanSNPer2 [INFO ]  Running CanSNPer2 version-2.0.6
2025-02-05 12:18:17,717 DatabaseConnection [DEBUG]  DatabaseConnection variables database: database/francisella_tularensis.db, verbose: None
2025-02-05 12:18:17,719 DatabaseConnection [INFO ]  database/francisella_tularensis.db opened successfully...
2025-02-05 12:18:17,719 DatabaseConnection [INFO ]  cursor created
2025-02-05 12:18:17,719 DatabaseConnection [DEBUG]  Database connected!
2025-02-05 12:18:17,719 DatabaseConnection [INFO ]  Load XMFAFunctions
Run 4 alignments to references using progressiveMauve
2025-02-05 12:18:17,720 CanSNPer2 [INFO ]  Running CanSNPer2 on FSC200.fasta
2025-02-05 12:18:17,720 CanSNPer2 [INFO ]  Run mauve alignments
2025-02-05 12:18:17,720 CanSNPer2 [INFO ]  Starting progressiveMauve on 5 references
2025-02-05 12:18:17,720 CanSNPer2 [DEBUG]  progressiveMauve --output /tmp/CanSNPer2/OSU18_FSC200.xmfa references//OSU18.fna test_data/FSC200.fasta
2025-02-05 12:18:17,724 CanSNPer2 [DEBUG]  progressiveMauve --output /tmp/CanSNPer2/FTNF002-00_FSC200.xmfa references//FTNF002-00.fna test_data/FSC200.fasta
2025-02-05 12:18:17,725 CanSNPer2 [DEBUG]  progressiveMauve --output /tmp/CanSNPer2/LVS_FSC200.xmfa references//LVS.fna test_data/FSC200.fasta
2025-02-05 12:18:17,726 CanSNPer2 [DEBUG]  progressiveMauve --output /tmp/CanSNPer2/SCHUS4.2_FSC200.xmfa references//SCHUS4.2.fna test_data/FSC200.fasta
2025-02-05 12:18:17,728 CanSNPer2 [DEBUG]  progressiveMauve --output /tmp/CanSNPer2/FSC200_FSC200.xmfa references//FSC200.fna test_data/FSC200.fasta
2025-02-05 12:18:17,766 CanSNPer2 [WARNI]  WARNING progressiveMauve finished with a exitcode: 11
2025-02-05 12:18:17,766 CanSNPer2 [DEBUG]  This progressiveMauve error is showing up for bad genomes containing short repetative contigs or sequence contains dashes
2025-02-05 12:18:17,769 CanSNPer2 [WARNI]  WARNING progressiveMauve finished with a exitcode: 11
2025-02-05 12:18:17,769 CanSNPer2 [DEBUG]  This progressiveMauve error is showing up for bad genomes containing short repetative contigs or sequence contains dashes
2025-02-05 12:18:17,771 CanSNPer2 [WARNI]  WARNING progressiveMauve finished with a exitcode: 11
2025-02-05 12:18:17,771 CanSNPer2 [DEBUG]  This progressiveMauve error is showing up for bad genomes containing short repetative contigs or sequence contains dashes
2025-02-05 12:18:17,774 CanSNPer2 [WARNI]  WARNING progressiveMauve finished with a exitcode: 11
2025-02-05 12:18:17,774 CanSNPer2 [DEBUG]  This progressiveMauve error is showing up for bad genomes containing short repetative contigs or sequence contains dashes
2025-02-05 12:18:17,777 CanSNPer2 [WARNI]  WARNING progressiveMauve finished with a exitcode: 11
2025-02-05 12:18:17,777 CanSNPer2 [DEBUG]  This progressiveMauve error is showing up for bad genomes containing short repetative contigs or sequence contains dashes
2025-02-05 12:18:17,777 CanSNPer2 [WARNI]  Mauve ran into an error with sequence test_data/FSC200.fasta may contain a dash, replace with N characters and retry mauve
2025-02-05 12:18:17,777 CanSNPer2 [DEBUG]  sed 's/-/N/g' test_data/FSC200.fasta > /tmp/CanSNPer2/FSC200.fasta.tmp
2025-02-05 12:18:17,790 CanSNPer2 [DEBUG]  New query: /tmp/CanSNPer2/FSC200.fasta.tmp
2025-02-05 12:18:17,790 CanSNPer2 [INFO ]  Starting progressiveMauve on 5 references
2025-02-05 12:18:17,790 CanSNPer2 [DEBUG]  progressiveMauve --output /tmp/CanSNPer2/OSU18_FSC200.xmfa references//OSU18.fna /tmp/CanSNPer2/FSC200.fasta.tmp
2025-02-05 12:18:17,791 CanSNPer2 [DEBUG]  progressiveMauve --output /tmp/CanSNPer2/FTNF002-00_FSC200.xmfa references//FTNF002-00.fna /tmp/CanSNPer2/FSC200.fasta.tmp
2025-02-05 12:18:17,792 CanSNPer2 [DEBUG]  progressiveMauve --output /tmp/CanSNPer2/LVS_FSC200.xmfa references//LVS.fna /tmp/CanSNPer2/FSC200.fasta.tmp
2025-02-05 12:18:17,793 CanSNPer2 [DEBUG]  progressiveMauve --output /tmp/CanSNPer2/SCHUS4.2_FSC200.xmfa references//SCHUS4.2.fna /tmp/CanSNPer2/FSC200.fasta.tmp
2025-02-05 12:18:17,794 CanSNPer2 [DEBUG]  progressiveMauve --output /tmp/CanSNPer2/FSC200_FSC200.xmfa references//FSC200.fna /tmp/CanSNPer2/FSC200.fasta.tmp
2025-02-05 12:18:17,811 CanSNPer2 [WARNI]  WARNING progressiveMauve finished with a exitcode: 11
2025-02-05 12:18:17,812 CanSNPer2 [DEBUG]  This progressiveMauve error is showing up for bad genomes containing short repetative contigs or sequence contains dashes
2025-02-05 12:18:17,814 CanSNPer2 [WARNI]  WARNING progressiveMauve finished with a exitcode: 11
2025-02-05 12:18:17,814 CanSNPer2 [DEBUG]  This progressiveMauve error is showing up for bad genomes containing short repetative contigs or sequence contains dashes
2025-02-05 12:18:17,819 CanSNPer2 [WARNI]  WARNING progressiveMauve finished with a exitcode: 11
2025-02-05 12:18:17,819 CanSNPer2 [DEBUG]  This progressiveMauve error is showing up for bad genomes containing short repetative contigs or sequence contains dashes
2025-02-05 12:18:17,835 CanSNPer2 [WARNI]  WARNING progressiveMauve finished with a exitcode: 11
2025-02-05 12:18:17,835 CanSNPer2 [DEBUG]  This progressiveMauve error is showing up for bad genomes containing short repetative contigs or sequence contains dashes
2025-02-05 12:18:17,877 CanSNPer2 [WARNI]  WARNING progressiveMauve finished with a exitcode: 11
2025-02-05 12:18:17,877 CanSNPer2 [DEBUG]  This progressiveMauve error is showing up for bad genomes containing short repetative contigs or sequence contains dashes
2025-02-05 12:18:17,877 CanSNPer2 [DEBUG]  []
2025-02-05 12:18:17,877 CanSNPer2 [DEBUG]  Mauve exited with a non zero exit status, continue with next sample!

CanSNPer2 was installed over :
mamba create -n cansnper2 cansnper2 (version 2.0.6)

Neither grepping for dash symbols
grep "-" sample.fasta
Nor grepping for any unusual symbols
grep -n "[^ACGTNacgtn>]" sample.fasta
has show anything out of the ordinary.

I've tried reducing the contig headers to simple forms
e.g. for one contig sequence >LVS
e.g. for multi contig Assembly >contig1, >contig2, ...
But nothing has shown an effect.

Am I missing something?
I'd really appreciate any ideas on what might be causing this.