atlas: MissingOutputException in line 82 of atlas/rules/qc.snakefile

Having some trouble with a missing output file for rule get_read_stats in qc.snakefile.

• I’m running atlas, version 2.0.1 installed via conda.
• I’m running on a local Linux server, 40 cores, 320GB RAM, 74 TB of disk space on a decently fast RAID array.

Here’s the log message:

[Wed Feb 27 13:10:46 2019]                                                                                              
rule get_read_stats:                                                                                                    
    input: NKS2/sequence_quality_control/NKS2_QC_R1.fastq.gz, NKS2/sequence_quality_control/NKS2_QC_R2.fastq.gz         
    output: NKS2/sequence_quality_control/read_stats/QC.zip, NKS2/sequence_quality_control/read_stats/QC_read_counts.tsv
    log: NKS2/logs/QC/read_stats/QC.log                                                                                 
    jobid: 74                                                                                                           
    wildcards: sample=NKS2, step=QC                                                                                     
    priority: 30                                                                                                        
    threads: 40                                                                                                         
    resources: mem=32, java_mem=27                                                                                      
                                                                                                                        
Dynamic output is deprecated in favor of checkpoints (see docs). It will be removed in Snakemake 6.0.                   
Dynamic output is deprecated in favor of checkpoints (see docs). It will be removed in Snakemake 6.0.                   
Dynamic output is deprecated in favor of checkpoints (see docs). It will be removed in Snakemake 6.0.                   
Dynamic output is deprecated in favor of checkpoints (see docs). It will be removed in Snakemake 6.0.                   
Dynamic output is deprecated in favor of checkpoints (see docs). It will be removed in Snakemake 6.0.                   
Dynamic output is deprecated in favor of checkpoints (see docs). It will be removed in Snakemake 6.0.                   
Waiting at most 5 seconds for missing files.                                                                            
MissingOutputException in line 82 of /home/ctmr/anaconda3/envs/metagenome-atlas/lib/python3.6/site-packages/atlas/rules/qc.snakefile:                                                                                                           
Missing files after 5 seconds:                                                                                          
NKS2/sequence_quality_control/read_stats/QC.zip                                                                         
NKS2/sequence_quality_control/read_stats/QC_read_counts.tsv                                                             
This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait.   
Shutting down, this might take some time.                                                                               
Exiting because a job execution failed. Look above for error message                                                    
Note the path to the log file for debugging.                                                                            
Documentation is available at: https://metagenome-atlas.readthedocs.io                                                  
Issues can be raised at: https://github.com/metagenome-atlas/atlas/issues                                               
Complete log: /home/ctmr/projects/039_NKSS/analyses/02.metagenome-atlas_20190227/.snakemake/log/2019-02-27T131043.97813.snakemake.log                                                                                                          
[2019-02-27 13:10 CRITICAL] Command 'snakemake --snakefile /home/ctmr/anaconda3/envs/metagenome-atlas/lib/python3.6/site-packages/atlas/Snakefile --directory /home/ctmr/projects/039_NKSS/analyses/02.metagenome-atlas_20190227 --printshellcmds --jobs 40 --rerun-incomplete --configfile '/home/ctmr/projects/039_NKSS/analyses/02.metagenome-atlas_20190227/config.yaml' --nolock  --use-conda  --conda-prefix /home/ctmr/db/metagenome-atlas/conda_envs   all   ' returned non-zero exit status 1.                                                                                                                 

Here’s what’s in the output folder:

(metagenome-atlas)$ tree NKS2/
NKS2/                                                                                 
├── logs                                                                              
│   ├── NKS2_quality_filtering_stats.txt                                              
│   └── QC                                                                            
│       ├── decontamination.log                                                       
│       ├── deduplicate.log                                                           
│       ├── init.log                                                                  
│       ├── quality_filter.log                                                        
│       └── read_stats                                                                
│           ├── clean.log                                                             
│           ├── deduplicated.log                                                      
│           ├── filtered.log                                                          
│           ├── QC.log                                                                
│           └── raw.log                                                               
└── sequence_quality_control                                                          
    ├── contaminants                                                                  
    │   ├── PhiX_R1.fastq.gz                                                          
    │   ├── PhiX_R2.fastq.gz                                                          
    │   └── PhiX_se.fastq.gz                                                          
    ├── NKS2_decontamination_reference_stats.txt                                      
    ├── NKS2_QC_R1.fastq.gz                                                           
    ├── NKS2_QC_R2.fastq.gz                                                           
    ├── NKS2_QC_se.fastq.gz                                                           
    └── read_stats                                                                    
        ├── clean_read_counts.tsv                                                     
        ├── clean.zip                                                                 
        ├── deduplicated_read_counts.tsv                                              
        ├── deduplicated.zip                                                          
        ├── filtered_read_counts.tsv                                                  
        ├── filtered.zip                                                              
        ├── raw_read_counts.tsv                                                       
        └── raw.zip                                                                   
                                                                                      
6 directories, 25 files                                                               

Here is the full log output from Snakemake: 2019-02-27T131043.978139.snakemake.log