[prophyle_propagation] 2021-08-06 20:08:37 Progress of k-mer propagation: 49987 / 49988                                                              
starting propagation for EPI_ISL_1000010-up62.full.fa.complete                                                                                       
"/Users/karel/miniconda/lib/python3.8/site-packages/prophyle/prophyle_assembler/prophyle_assembler" -S -k 31 -x ./EPI_ISL_1000010-up62.full.fa -i ./E
PI_ISL_1001388-up31.full.fa -i ./EPI_ISL_1000010-up61.full.fa -o ./EPI_ISL_1001388-up31.reduced.fa -o ./EPI_ISL_1000010-up61.reduced.fa -s ./EPI_ISL_
1000010-up62.count.tsv                                                    
[prophyle_propagation] 2021-08-06 20:08:38 Progress of k-mer propagation: 49988 / 49988                                                              
ln -s ./EPI_ISL_1000010-up62.full.fa ./EPI_ISL_1000010-up62.reduced.fa                                                                               
[prophyle] 2021-08-06 20:08:40 Finished (325.5 MB used): make -j 8 -C results/post/covid/propagation V=1
[prophyle] 2021-08-06 20:08:40 Propagation post-processing                                                                                           
[prophyle] 2021-08-06 20:08:40 Shell command: cat results/post/covid/propagation/*.tsv > results/post/covid/index.fa.kmers.tsv
/bin/bash: /bin/cat: Argument list too long                               
[prophyle] 2021-08-06 20:08:42 Unfinished, an error occurred (error code 1, 7.4 MB used): cat results/post/covid/propagation/*.tsv > results/post/cov
id/index.fa.kmers.tsv                                                     
Error: K-mer statistics could not be created.                             
Traceback (most recent call last):                                        
  File "/Users/karel/miniconda/bin/prophyle", line 11, in <module>                                                                                   
    sys.exit(main())                                                      
  File "/Users/karel/miniconda/lib/python3.8/site-packages/prophyle/prophyle.py", line 1497, in main
    prophyle_index(                                                       
  File "/Users/karel/miniconda/lib/python3.8/site-packages/prophyle/prophyle.py", line 715, in prophyle_index
    _propagation_postprocessing(index_dir, index_tree_1, index_tree_2)                                                                               
  File "/Users/karel/miniconda/lib/python3.8/site-packages/prophyle/prophyle.py", line 507, in _propagation_postprocessing
    pro.run_safe(                                                         
  File "/Users/karel/miniconda/lib/python3.8/site-packages/prophyle/prophylelib.py", line 486, in run_safe
    raise RuntimeError("A command failed, see messages above.")                                                                                      
RuntimeError: A command failed, see messages above.                                                                                                  
[Fri Aug  6 20:08:42 2021]                                                
Error in rule prophyle_index:                                             
    jobid: 100002                                                         
    output: results/post/covid, results/post/covid/propagation                                                                                       
    shell:                                                                
                                                                          
        prophyle index -k31 -T -A -g results/asm/covid results/tree/covid.nw results/post/covid
                                                                          
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
                                                                          
Removing output files of failed job prophyle_index since they might be corrupted:                                                                    
results/post/covid, results/post/covid/propagation                                                                                                   
Job failed, going on with independent jobs.                               
Exiting because a job execution failed. Look above for error message                                                                                 
Complete log: /Users/karel/github/my/mof-compress-covid/.snakemake/log/2021-08-06T133916.040096.snakemake.log
make: *** [all] Error 1