Setup results missing

[vrohnie]

Hey there,

Just wanted to try out your phylogenomics pipeline, however I didn't get very far:

I ran the following:

./phylociraptor setup -t local --config-file ~/data/Analyses/2024/202505_X_Schizo/phylociraptor/config.yaml

with output: 2024-05-07 11:50 - Welcome to phylociraptor setup v1.0.0 2024-05-07 11:50 - Singularity version: 4.1.2 2024-05-07 11:50 - Snakemake version: 6.0.2

When I try to run:

./phylociraptor orthology -t local --config-file ~/data/Analyses/2024/202505_X_Schizo/phylociraptor/config.yaml

I get the following error:

2024-05-07 11:51 - Welcome to phylociraptor orthology v1.0.0 2024-05-07 11:51 - Singularity version: 4.1.2 2024-05-07 11:51 - Snakemake version: 6.0.2 2024-05-07 11:51 - ERROR: Some files are missing preventing this part to run. 2024-05-07 11:51 - Did you run setup which is required by this step? 2024-05-07 11:51 - Missing file: results/checkpoints/modes/phylogenomics_setup.done

Head of teh config file:

general settings:

species: "~/data/Analyses/2024/202505_X_Schizo/phylociraptor/genomes_bigyra.csv" email: "veronika.schusterbauer@bisy.at" #this is used during genome download to communicate with the NCBI database. concurrency: 20 # certain steps can be divided into batches to speed up computation. Here you can give the number of batches. seed: "1987" #(optional) random seed number to increase reproducibility of iqtree and raxml runs. default: none (=random).

settings related to busco

orthology: method: "busco" threads: 32 busco_options: set: "eukaryota_odb10" version: "5.2.1" #possible is "3.0.2" or "5.2.1" mode: "genome" augustus_species: #Together with BUSCO 5 this is optional and will use augustus instead of metaeuk. Mandatory for BUSCO 3 (there is no metaeuk) additional_parameters: ""

head of the csv: species,Assembly Name,Organism Infraspecific Names Strain,Assembly Stats Total Sequence Length,Assembly Level,Assembly Release Date,WGS project accession,Assembly Accession,web_local Blastocystis hominis,ASM15166v1,,18817245,Scaffold,2010-07-06,CABX01,GCA_000151665.1,web=GCA_000151665.1 Blastocystis hominis,ASM15166v1,,18817245,Scaffold,2010-07-06,CABX01,GCF_000151665.1,web=GCF_000151665.1 Aurantiochytrium limacinum,Aurantiochytrium limacinum BL10 v1,BL10,60288329,Contig,2024-02-26,JAVCPM01,GCA_036850685.1,web=GCA_036850685.1 Cafeteria roenbergensis,CrBVI,BVI,36283887,Contig,2019-09-09,VLTN01,GCA_008330645.1,web=GCA_008330645.1 Proteromonas lacertae,ASM224513v1,LA,52192279,Contig,2017-08-09,NGBS01,GCA_002245135.1,web=GCA_002245135.1 Blastocystis sp. subtype 4,ASM74375v1,WR1,12919355,Scaffold,2014-09-29,JPUL02,GCA_000743755.1,web=GCA_000743755.1 Blastocystis sp. subtype 4,ASM74375v1,WR1,12919355,Scaffold,2014-09-29,JPUL02,GCF_000743755.1,web=GCF_000743755.1 Schizochytrium sp. CCTCC M209059,ASM81894v1,CCTCC M209059,39089698,Scaffold,2015-01-15,JTFK01,GCA_000818945.1,web=GCA_000818945.1 Blastocystis sp. subtype 3,ASM2544941v1,,12118208,Scaffold,2022-09-28,JANPWR01,GCA_025449415.1,web=GCA_025449415.1

Since I'm not getting any error message, could you possibly pinpoint me, as to where I'm going wrong?

Best regards, Veronika

[reslp]

Hi Veronika,

Can you please run phylociraptor setupwith the additional --debug flag and post the output here? Maybe this way we can better diagnose what went wrong.

Many thanks!

best,

Philipp

[vrohnie]

Hey,

Thanks for the swift response.

the debug output makes the problem rather obvious. Snakemake does not like relative paths.

However, I guess I would change my request then to forward error messages to stdout without the --debug flag active ;)

Here is the output (for completeness):

2024-05-07 14:25 - Welcome to phylociraptor setup v1.0.0 2024-05-07 14:25 - Singularity version: 4.1.2 2024-05-07 14:25 - Snakemake version: 6.0.2 2024-05-07 14:25 - DEBUG: flags: {'force': False, 'FORCE': False, 'cluster': 'local', 'cluster_config': None, 'dry': False, 'help': False, 'verbose': False, 'si_args': '', 'sm_args': '', 'rerun': False, 'unlock': False, 'debug': True, 'config_file': '/home/vrohnie/data/Analyses/2024/202505_X_Schizo/phylociraptor/config.yaml', 'samples_file': None, 'busco_set': None, 'add_genomes': False} 2024-05-07 14:25 - DEBUG: Additional flags will be passed on to snakemake: -p Building DAG of jobs... MissingInputException in line 86 of /home/vrohnie/Programs/phylociraptor/rules/setup.smk: Missing input files(Using '~' in your paths is not allowed as such platform specific syntax is not resolved by Snakemake. In general, try sticking to relative paths for everything inside the working directory.) for rule download_genomes: ~/data/Analyses/2024/202505_X_Schizo/phylociraptor/genomes_bigyra.csv 2024-05-07 14:25 - DEBUG: snakemake -p -s rules/setup.smk --use-singularity -r setup --latency-wait 10 --cores --configfile /home/vrohnie/data/Analyses/2024/202505_X_Schizo/phylociraptor/config.yaml -p --singularity-args -B $(pwd)/.usr_tmp/:/usertmp

[vrohnie]

Thanks, will come back if run into other problems.

Best, Veronika