Problem at step "REMOVING UNTRUSTED K - MERS"

[sashulkaSh]

Hello!
I run:

reckoner -genome 4500000000 -prefix ${p} -threads 128 -kmcmemory 900 -longkmer -verbose -reuse ${r1} ${r2}

RECKONER ver. 2.1                                                                                                                                                                                          
                                                                                                                                                                                                           
##################################################                                                                                                                                                         
INPUT DATA SUMMARY                                                                                                                                                                                         
##################################################                                                                                                                                                         
Read file 1                                                                                                                                                                                                
      Name                    :  1.trim.fq                                                                                                                   
      Compressed              : no                                                                                                                                                                         
Read file 2                                                                                                                                                                                                
      Name                    : 2.trim.fq                                                                                                                   
      Compressed              : no                                                                                                                                                                         
Log file name                 : 1.log                                                                                                                        
K-mer length                  : not defined (will be determined automatically)                                                                                                                             
Long k-mer length             : not defined (will be determined automatically)                                                                                                                             
Number of threads             : 128                                                                                                                                                                        
                                                                                                                                                                                                           
##################################################                                                                                                                                                         
CHECKING READS                                                                                                                                                                                             
##################################################                                                                                                                                                         
1.trim.fq                                                                                                                                                   
     Quality score offset          : 33                                                                                                                                                                    
2.trim.fq                                                                                                                                                   
     Quality score offset          : 33                                                                                                                                                                    
                                                                                                                                                                                                           
##################################################                                                                                                                                                         
DETERMINING PARAMETERS                                                                                                                                                                                     
##################################################                                                                                                                                                         
Determined k-mer length: 32                                                                                                                                                                                
Determined long k-mer length: 48                                                                                                                                                                           
                                                                                                                                                                                                           
##################################################                                                                                                                                                         
K - MER COUNTING                                                                                                                                                                                           
##################################################                                                                                                                                                         
Error: some error while reading suffix file                                                                                                                                                                
At least one of the KMC databases does not exist. Both of them will be created.                                                                                                                            
                                                                                                                                                                                                           
***********************************************************************************************************************************************************************************************************
*********************************************************************                                                                                                                                      
Stage 1: 100%                                                                                                                                                                                              
Stage 2: 100%
1st stage: 285.866s                               
2nd stage: 310.003s   
Total    : 595.869s                         
Tmp size : 244856MB                                                                                  
                                                                                                     
Stats: 
   No. of k-mers below min. threshold :  31749099169
   No. of k-mers above max. threshold :            0                                                                                                                                                       
   No. of unique k-mers               :  37137077307                                                                                                                                                       
   No. of unique counted k-mers       :   5387978138                                                                                                                                                       
   Total no. of k-mers                : 250142374748                                                                                                                                                       
   Total no. of reads                 :   1524476080
   Total no. of super-k-mers          :  20070135337
***********************************************************************************************************************************************************************************************************
*********************************************************************
Stage 1: 43%



Stage 1: 44%
Stage 1: 100%
Stage 2: 100%
1st stage: 281.839s
2nd stage: 367.553s
Total    : 649.392s
Tmp size : 207319MB

Stats:
   No. of k-mers below min. threshold :            0
   No. of k-mers above max. threshold :            0
   No. of unique k-mers               :  45200870921
   No. of unique counted k-mers       :  45200870921
   Total no. of k-mers                : 225731535323
   Total no. of reads                 :   1524476080
   Total no. of super-k-mers          :  11519864474

################################################## 
DETERMINING CUTOFF THRESHOLD
################################################## 
Cutoff: 5

################################################## 
REMOVING UNTRUSTED K - MERS
################################################## 
in1: 0% 

then RECKONER does nothing, I left the program for a few days, nothing changed

In the top (or htop), I see that the program does not use resources

what is my problem? pls, help!

(files, that were created:
1.kmc_pre
1.kmc_suf
1.log
1.long.kmc_pre
1.long.kmc_suf
1.lst
1.tmp.kmc_pre
1.tmp.kmc_suf
)

[maciejdlugosz]

@sashulkaSh
Thank you for reporting the problem. Please, give a size of created kmc_pre/kmc_suf files, size of the input FASTQ files and amount of free HDD space.

[sashulkaSh]

4 1.kmc_pre
4 1.kmc_suf
258M 1.long.kmc_pre
464G 1.long.kmc_suf
258M 1.tmp.kmc_pre
36G 1.tmp.kmc_suf
PE reads - 319G *2
64T free space
RAM 1T

[maciejdlugosz]

@sashulkaSh
I'm not able to infer, what is the reason of the problem. Can you give asccession number? And, as I see, the reads are trimmed - what is a strategy of trimming?