hyphens in sample names causing "snakemake invocation error"

[hehouts]

I have a 32 virome-metagenomes (not downloaded from the sra) that have hyphens in the sample name (e.g. SM-6OSOR, SM-6UG79, SM-6WJN6) in /home/hehouts/dynamic-duos-virome/grist/Archive/outputs.s5_vir/abundtrim/.

I tried running grist with genome-grist run config_s5_vir.yml summarize_mapping -j8
with config_s5_vir.yml:

prevent_sra_download: true                                                                                                                    
samples:                                                                                                                                      
- SM-6UG79                                                                                                                                                                                                                                                                 
- SM-7I1G8                                                                                                                                    
- SM-7K25Z   
# ...ect  
                                                                                                                               
outdir: outputs.s5_vir                                                                                                                        
                                                                                                       
prefetch_memory: 20e9                                                                                                                                                                                                                               
                                                                                                                                              
sourmash_database_ksize: 21                                                                                                                   
sourmash_scaled: 200                                                                                                                          
sourmash_database_threshold_bp: 100                                                                                                           
                                                                                                                                              
sourmash_databases:                                                                                                                           
- /group/ctbrowngrp/scratch/ctbrown/gut-phage-db.grist/GPD_sequences.zip                                                                      
                                                                                                                                              
local_databases_info:                                                                                                                         
- /group/ctbrowngrp/scratch/ctbrown/gut-phage-db.grist/GPD_sequences.info.csv                                                                 
                                                                                                                                              
taxonomies:                                                                                                                                   
- /group/ctbrowngrp/genbank/all_genbank_lineages.20200727.csv    

its returning an error:

MissingInputException in line 410 of /home/hehouts/miniconda3/envs/grist/lib/python3.9/site-packages/genome_grist/conf/Snakefile:             
Missing input files for rule summarize_mapping:     
outputs.s5_vir/reports/report-mapping-SM-6OSOR.html                                                                                           
outputs.s5_vir/reports/report-mapping-SM-7IL1E.html                                                                                           
outputs.s5_vir/reports/report-gather-SM-7K25Z.html     
... ect ...
Error in snakemake invocation: Command '['snakemake', '-s', '/home/hehouts/miniconda3/envs/grist/lib/python3.9/site-packages/genome_grist/conf
/Snakefile', '-j', '1', '--use-conda', 'summarize_mapping', '--rerun-incomplete', '-j8', '--configfile', '/home/hehouts/miniconda3/envs/grist/
lib/python3.9/site-packages/genome_grist/conf/defaults.conf', '/home/hehouts/miniconda3/envs/grist/lib/python3.9/site-packages/genome_grist/co
nf/system.conf', 'config_s5_vir.yml']' returned non-zero exit status 1.

I think its weird that is I run genome-grist run config_s5_vir.yml smash_reads -n, I get a similar error:

MissingInputException in line 195 of /home/hehouts/miniconda3/envs/grist/lib/python3.9/site-packages/genome_grist/conf/Snakefile:
Missing input files for rule smash_reads:
outputs.s5_vir/sigs/SM-7I1G8.abundtrim.sig.gz
outputs.s5_vir/sigs/SM-7K25Z.abundtrim.sig.gz
...ect
Error in snakemake invocation: Command '['snakemake', '-s', '/home/hehouts/miniconda3/envs/grist/lib/python3.9/site-packages/genome_grist/conf/Snakefile', '-j', '1', '--use-conda', 'smash_reads', '-n', '--configfile', '/home/hehouts/miniconda3/envs/grist/lib/python3.9/site-packages/genome_grist/conf/defaults.conf', '/home/hehouts/miniconda3/envs/grist/lib/python3.9/site-packages/genome_grist/conf/system.conf', 'config_s5_vir.yml']' returned non-zero exit status 1.

but if I run genome-grist run config_s5_vir.yml trim_reads -n
it recognizes that the input files are there:

samples: ['SM-6UG79', 'SM-71WY3', 'SM-7CRX4', 'SM-6X9WV', 'SM-76CAU', 'SM-7CP3H', 'SM-7EWTT', 'SM-6OSOR', 'SM-6Y2V3', 'SM-77VQ4', 'SM-7EWUL', 'SM-6WJN6', 'SM-6X9X4', 'SM-6YAZO', 'SM-6ZKSM', 'SM-71WXM', 'SM-73JY4', 'SM-76EOJ', 'SM-791BX', 'SM-7BF2J', 'SM-7CRJ8', 'SM-7EWUH', 'SM-7GYJO', 'SM-7IL1E', 'SM-7KPUR', 'SM-7MOQJ', 'SM-6WOCE', 'SM-6ZEVI', 'SM-7AA2E', 'SM-7BP5L', 'SM-7I1G8', 'SM-7K25Z']
outdir: outputs.s5_vir
Building DAG of jobs...
Nothing to be done (all requested files are present and up to date).

I tried changing the sample names to use underscores instead of hyphens, in /home/hehouts/dynamic-duos-virome/grist/Archive/outputs.virtest/abundtrim & its config /home/hehouts/dynamic-duos-virome/grist/Archive/config_virtest.yml and it appears to be working!

So it seems like the hyphens are causing the problem.

[ctb]

I will check! the filenames do look right. <sigh> :)

[ctb]

Results of my investigation match yours! Hyphens don't work, underscores do. Wat?

[ctb]

Figured it out: #188.