VCF file is empty

[Axze-rgb]

Describe the bug
The vcf file is empty, calling in individual (germline) mode

Version

$ octopus --version
[2023-09-12 20:51:11] <INFO> ------------------------------------------------------------------------
[2023-09-12 20:51:11] <INFO> octopus v0.7.4 (ed012a6e)
[2023-09-12 20:51:11] <INFO> Copyright (c) 2015-2021 University of Oxford
[2023-09-12 20:51:11] <INFO> ------------------------------------------------------------------------
[2023-09-12 20:51:11] <EROR> A user error has occurred:
[2023-09-12 20:51:11] <EROR> 
[2023-09-12 20:51:11] <EROR>     The option you specified '--version' is not recognised.
[2023-09-12 20:51:11] <EROR> 
[2023-09-12 20:51:11] <EROR> To help resolve this error use the --help command to view required and
[2023-09-12 20:51:11] <EROR> allowable options.
[2023-09-12 20:51:11] <INFO> ------------------------------------------------------------------------

Command
Command line to install octopus:

git clone https://github.com/luntergroup/octopus.git
scripts/install.py  #all dependencies were in the PATH

Command line to run octopus:

octopus -R vaga.fa --threads 22 -C individual  -P 2 -B 64Gb -I ancestor.sorted.bam  -o Octopus_call/test.vcf.gz --bad-region-tolerance LOW --consider-unmapped-reads --min-supporting-reads 3 --forest-model /home/alessandro/software/octopus/resources/forests/germline.v0.7.4.forest.gz

Additional context
just a normal fasta with a bam obtained from mapping with bwa-mem
bwa command:

while read p; do bwa-mem2 mem -R '@RG\tID:foo\tSM:bar' -k 12 -t22 vaga.fa ${p}.R1.fastq.gz ${p}.R2.fastq.gz|samtools sort -m 2G -@24 -o bwa_k10_mapping/${p}.sorted.bam; done <ID

Any idea as why my vcf is empty? The run time is also extremely short, less than 5 minutes, which I find surprising. It makes me the impression it's skipping steps it shouldn't.

I checked a pileup, just in case there would be 0 variant in the alignement (which wouldn't make any sense but who knows, maybe a wrong manipulation), but there are variants.

I can send you the bam file if you wish so.

Thanks a lot

EDIT: removing the -C tag seems to solve the issue. That being said, the time estimate for the analysis is very long. Is there anyway to speed things up?

[2023-09-12 21:33:28] <INFO> ------------------------------------------------------------------------
[2023-09-12 21:51:19] <INFO> Chrom_1:3107486             0.5%          17m 50s            2d 11h
[2023-09-12 21:55:49] <INFO> Chrom_1:4596832             1.0%          22m 21s            1d 12h
[2023-09-12 22:00:20] <INFO> Chrom_3:5244696             1.5%          26m 52s             1d 5h
[2023-09-12 22:01:11] <INFO> Chrom_3:15532716            1.6%          27m 42s             1d 4h
[2023-09-12 22:02:13] <INFO> Chrom_3:15535861            1.7%          28m 44s             1d 3h
[2023-09-12 22:03:06] <INFO> Chrom_1:4640543             1.8%          29m 37s             1d 2h
[2023-09-12 22:04:12] <INFO> Chrom_3:2097164             1.9%          30m 43s             1d 2h
[2023-09-12 22:05:01] <INFO> Chrom_3:9709436             2.0%          31m 33s             1d 1h
[2023-09-12 22:05:37] <INFO> Chrom_3:17116716            2.1%           32m 9s           24h 57m
[2023-09-12 22:06:36] <INFO> Chrom_1:4655724             2.2%           33m 7s           24h 31m
[2023-09-12 22:07:31] <INFO> Chrom_1:8911072             2.3%           34m 2s            24h 4m
[2023-09-12 22:08:31] <INFO> Chrom_1:10322451            2.4%           35m 2s           23h 43m
[2023-09-12 22:09:29] <INFO> Chrom_3:8281491             2.5%              36m           23h 23m
[2023-09-12 22:10:27] <INFO> Chrom_1:10323600            2.6%          36m 59s            23h 4m

EDIT; there might be an issue with the uploaded forest file, see here: #259 (comment)
is it the correct file?

EDIT: indeed the forest files can't be downloaded because of data size on github, therefore Octopus in forest mode has nothing to classify anything.