Getting stuck on spades-hammer

[AroArz]

Hello, I've used SPAdes to assemble my metagenomic datasets however two of my samples are getting stuck in the exact same place repeatedly. I was able to assemble all my samples using megahit without any issues but much prefer SPAdes.

18_R1.filtered_human.fq.gz      -2      /home/ctmr/projects/Aron/SPAdes/input/PA18_R2.filtered_human.fq.gz      --meta  -t      16

System information:
  SPAdes version: 3.13.1
  Python version: 3.6.7
  OS: Linux-3.10.0-862.14.4.el7.x86_64-x86_64-with-redhat-7.6-Nitrogen

Output dir: /home/ctmr/projects/Aron/SPAdes/output/PA18
Mode: read error correction and assembling
Debug mode is turned OFF

Dataset parameters:
  Metagenomic mode
  Reads:
    Library number: 1, library type: paired-end
      orientation: fr
      left reads: ['/home/ctmr/projects/Aron/SPAdes/input/PA18_R1.filtered_human.fq.gz']
      right reads: ['/home/ctmr/projects/Aron/SPAdes/input/PA18_R2.filtered_human.fq.gz']
      interlaced reads: not specified
      single reads: not specified
      merged reads: not specified
Read error correction parameters:
  Iterations: 1
  PHRED offset will be auto-detected
  Corrected reads will be compressed
Assembly parameters:
  k: [21, 33, 55]
  Repeat resolution is enabled
  Mismatch careful mode is turned OFF
  MismatchCorrector will be SKIPPED
  Coverage cutoff is turned OFF
Other parameters:
  Dir for temp files: /home/ctmr/projects/Aron/SPAdes/output/PA18/tmp
  Threads: 16
  Memory limit (in Gb): 250


======= SPAdes pipeline started. Log can be found here: /home/ctmr/projects/Aron/SPAdes/output/PA18/spades.log


===== Read error correction started.


== Running read error correction tool: /home/ctmr/projects/Aron/SPAdes/.snakemake/conda/edf7c82d/bin/spades-hammer /home/ctmr/projects/Aron/SPAdes/output/PA18/corrected/configs/config.info

  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  75)   Starting BayesHammer, built from N/A, git revision N/A
  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  76)   Loading config from /home/ctmr/projects/Aron/SPAdes/output/PA18/corrected/configs/config.info
  0:00:00.006     4M / 4M    INFO    General                 (main.cpp                  :  78)   Maximum # of threads to use (adjusted due to OMP capabilities): 16
  0:00:00.006     4M / 4M    INFO    General                 (memory_limit.cpp          :  49)   Memory limit set to 250 Gb
  0:00:00.006     4M / 4M    INFO    General                 (main.cpp                  :  86)   Trying to determine PHRED offset
  0:00:00.018     4M / 4M    INFO    General                 (main.cpp                  :  92)   Determined value is 33
  0:00:00.030     4M / 4M    INFO    General                 (hammer_tools.cpp          :  36)   Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ]
  0:00:00.031     4M / 4M    INFO    General                 (main.cpp                  : 113)   Size of aux. kmer data 24 bytes
     === ITERATION 0 begins ===
  0:00:00.031     4M / 4M    INFO   K-mer Counting           (kmer_data.cpp             : 280)   Estimating k-mer count
  0:00:00.200   260M / 260M  INFO   K-mer Counting           (kmer_data.cpp             : 285)   Processing /home/ctmr/projects/Aron/SPAdes/input/PA18_R1.filtered_human.fq.gz
  0:00:34.945   320M / 320M  INFO   K-mer Counting           (kmer_data.cpp             : 294)   Processed 12646899 reads
  0:00:34.946   320M / 320M  INFO   K-mer Counting           (kmer_data.cpp             : 285)   Processing /home/ctmr/projects/Aron/SPAdes/input/PA18_R2.filtered_human.fq.gz
  0:01:08.169   320M / 320M  INFO   K-mer Counting           (kmer_data.cpp             : 294)   Processed 25293798 reads
  0:01:08.169   320M / 320M  INFO   K-mer Counting           (kmer_data.cpp             : 299)   Total 25293798 reads processed
  0:01:08.803   320M / 320M  INFO   K-mer Counting           (kmer_data.cpp             : 306)   Estimated 255030583 distinct kmers
  0:01:08.834    64M / 320M  INFO   K-mer Counting           (kmer_data.cpp             : 311)   Filtering singleton k-mers
37 8 0
nslots: 536870912
bits per slot: 8 range: 0000002000000000
  0:01:08.834   716M / 716M  INFO   K-mer Counting           (kmer_data.cpp             : 317)   Processing /home/ctmr/projects/Aron/SPAdes/input/PA18_R1.filtered_human.fq.gz
  0:05:59.589   716M / 716M  INFO   K-mer Counting           (kmer_data.cpp             : 326)   Processed 12646899 reads
  0:05:59.589   716M / 716M  INFO   K-mer Counting           (kmer_data.cpp             : 317)   Processing /home/ctmr/projects/Aron/SPAdes/input/PA18_R2.filtered_human.fq.gz

Appreciate any help you can provide

[AroArz]

Just saw there were other posts on here notifying of similar issues (#152), I'm guessing they're the same but I'll let you be the judge of that.

Someone posted splitting the assembler and and spades-hammer (bhattlab/bhattlab_workflows#24) as a potential work around. I'll give that a try.

If you feel there is nothing more to add to this issue please feel free to close otherwise I'll await your reply.

[franciscozorrilla]

Did you do any sort of quality control/trimming before running metaspades? I was having this same issue with some of my samples WITH quality filtering using fastp, and after trying again WITHOUT quality filtering then all my samples finished assembly successfully

[Hyll1120]

Have you resolve the problem? I meet the same situation.