Hey guys! I have an issue with METASPADES running error correction forever on the reverse read. https://www.biostars.org/p/314891/ This basically describes my issues. Anyone familiar with this error? Another post suggests "--only-assembler" for metaspades to disable bayeshammer. Any experience with this? Context: Other samples ran just fine and It would be a shame if I couldn't get the last 3 samples to run and if I had to disable metaspades.

INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred


== Warning ==  output dir is not empty! Please, clean output directory before run.


Command line: /opt/conda/bin/spades.py	--meta	--threads	128	--memory	250	-1	/tmp/magfr926-2866718/nxf.DbwBv8ex5M/IBD00100_run0_phix_removed.unmapped_1.fastq.gz	-2	/tmp/magfr926-2866718/nxf.DbwBv8ex5M/IBD00100_run0_phix_removed.unmapped_2.fastq.gz	-o	/tmp/magfr926-2866718/nxf.DbwBv8ex5M	

System information:
  SPAdes version: 4.1.0
  Python version: 3.13.2
  OS: Linux-5.14.0-611.30.1.el9_7.x86_64-x86_64-with-glibc2.39

Output dir: /tmp/magfr926-2866718/nxf.DbwBv8ex5M
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: ['/tmp/magfr926-2866718/nxf.DbwBv8ex5M/IBD00100_run0_phix_removed.unmapped_1.fastq.gz']
      right reads: ['/tmp/magfr926-2866718/nxf.DbwBv8ex5M/IBD00100_run0_phix_removed.unmapped_2.fastq.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
  Assembly graph output will use GFA v1.2 format
Other parameters:
  Dir for temp files: /tmp/magfr926-2866718/nxf.DbwBv8ex5M/tmp
  Threads: 128
  Memory limit (in Gb): 250


======= SPAdes pipeline started. Log can be found here: /tmp/magfr926-2866718/nxf.DbwBv8ex5M/spades.log

/tmp/magfr926-2866718/nxf.DbwBv8ex5M/IBD00100_run0_phix_removed.unmapped_1.fastq.gz: max reads length: 101
/tmp/magfr926-2866718/nxf.DbwBv8ex5M/IBD00100_run0_phix_removed.unmapped_2.fastq.gz: max reads length: 101

Reads length: 101


===== Before start started. 


===== Read error correction started. 


===== Read error correction started. 


== Running: /opt/conda/bin/spades-hammer /tmp/magfr926-2866718/nxf.DbwBv8ex5M/corrected/configs/config.info

  0:00:00.001     1M / 21M   INFO    General                 (main.cpp                  :  76)   Starting BayesHammer, built from N/A, git revision N/A
  0:00:00.021     1M / 21M   INFO    General                 (main.cpp                  :  77)   Loading config from "/tmp/magfr926-2866718/nxf.DbwBv8ex5M/corrected/configs/config.info"
  0:00:00.031     1M / 21M   INFO    General                 (main.cpp                  :  79)   Maximum # of threads to use (adjusted due to OMP capabilities): 128
  0:00:00.032     1M / 21M   INFO    General                 (memory_limit.cpp          :  55)   Memory limit set to 250 Gb
  0:00:00.032     1M / 21M   INFO    General                 (main.cpp                  :  87)   Trying to determine PHRED offset
  0:00:00.033     1M / 21M   INFO    General                 (main.cpp                  :  93)   Determined value is 33
  0:00:00.033     1M / 21M   INFO    General                 (hammer_tools.cpp          :  40)   Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ]
  0:00:00.034     1M / 21M   INFO    General                 (main.cpp                  : 114)   Size of aux. kmer data 24 bytes
     === ITERATION 0 begins ===
  0:00:00.034     1M / 21M   INFO   K-mer Counting           (kmer_data.cpp             : 284)   Estimating k-mer count
  0:00:00.235  2049M / 2140M INFO   K-mer Counting           (kmer_data.cpp             : 289)   Processing "/tmp/magfr926-2866718/nxf.DbwBv8ex5M/IBD00100_run0_phix_removed.unmapped_1.fastq.gz"
  0:00:34.044  2049M / 2140M INFO   K-mer Counting           (kmer_data.cpp             : 298)   Processed 9541105 reads
  0:00:34.046  2049M / 2140M INFO   K-mer Counting           (kmer_data.cpp             : 289)   Processing "/tmp/magfr926-2866718/nxf.DbwBv8ex5M/IBD00100_run0_phix_removed.unmapped_2.fastq.gz"
  0:01:08.129  2049M / 2140M INFO   K-mer Counting           (kmer_data.cpp             : 298)   Processed 19082210 reads
  0:01:08.133  2049M / 2140M INFO   K-mer Counting           (kmer_data.cpp             : 303)   Total 19082210 reads processed
  0:01:10.515  2049M / 2140M INFO   K-mer Counting           (kmer_data.cpp             : 306)   Estimated 256349508 distinct kmers
  0:01:10.516     1M / 2140M INFO   K-mer Counting           (kmer_data.cpp             : 310)   Filtering singleton k-mers
  0:01:10.582   653M / 2140M INFO   K-mer Counting           (kmer_data.cpp             : 316)   Processing "/tmp/magfr926-2866718/nxf.DbwBv8ex5M/IBD00100_run0_phix_removed.unmapped_1.fastq.gz"
  0:04:55.238   654M / 2140M INFO   K-mer Counting           (kmer_data.cpp             : 325)   Processed 9541105 reads
  0:04:55.240   653M / 2140M INFO   K-mer Counting           (kmer_data.cpp             : 316)   Processing "/tmp/magfr926-2866718/nxf.DbwBv8ex5M/IBD00100_run0_phix_removed.unmapped_2.fastq.gz"

I vaguely remember this being reported somewhere else recently... @Ruiqi Li was it you?

yes it is a SPAdes bug

@Ruiqi Li Aye, not going crazy then. How did you resolve it? Did you just deactivate spades (would be a shame), or did you use "--only-assembler" ?? Thanks for your response in advance!

there is no way to resolve this, it is a spades bug

"there is no way to resolve this, it is a spades bug" What do you mean 😄 This is not true as a blanket statement. But still thanks for responding 🙂 Just means I wont try get metaspades to work on my dataset

Iirc The developers of spades said it was a very difficult bug to resolve and they were somewhat reluctant

That sounds a bit lazy 😄 but maybe im needlessly judgemental