error at the assembly stage

[Mewgia]

Description of the bug

Dear colleagues,
I have a question similar to that #198 when trying to launch test experiment.
nextflow
run nf-core/viralrecon
-profile test,docker -r 2.4.1
--outdir /work/viralrecon
The text of the error is in file. Similar to the question from the link above I've tried to skip assembly stage:
nextflow
run nf-core/viralrecon
-profile test,docker -r 2.4.1
--skip_assembly
--outdir /work/viralrecon
In this case, everything works fine, but I'd like to fix assembly error. Hope for your help.

Command used and terminal output

nextflow \
run nf-core/viralrecon \
-profile test,docker -r 2.4.1 \
--outdir /work/viralrecon

nextflow \
run nf-core/viralrecon \
-profile test,docker -r 2.4.1 \
--skip_assembly \
--outdir /work/viralrecon

Relevant files

error.txt

System information

Debian 5.10.103-1 (2022-03-07) x86_64, Nextflow 21.10.6.
Docker, viralrecon 2.4.1

[drpatelh]

Hi @Mewgia ! I have seen this error too and I still haven't got to the bottom of it. For some reason SPAdes fails when I run the pipeline on my laptop with the error below:

Error: SPAdes crashed! Please view spades.log for more information.

If you use --assemblers 'spades,minia' then this willbypass running Unicycler and the pipeline should finish.

[drpatelh]

This is what I see:

$ cat .command.log

tput: No value for $TERM and no -T specified
tput: No value for $TERM and no -T specified
tput: No value for $TERM and no -T specified

Starting Unicycler (2022-07-11 18:03:04)
    Welcome to Unicycler, an assembly pipeline for bacterial genomes. Since you
provided only short reads, Unicycler will essentially function as a SPAdes-
optimiser. It will try many k-mer sizes, choose the best based on contig length
and graph connectivity, and scaffold the graph using SPAdes repeat resolution.
    For more information, please see https://github.com/rrwick/Unicycler

Command: /usr/local/bin/unicycler --threads 2 -1 SAMPLE2_PE.primer_trim_1.fastq.gz -2 SAMPLE2_PE.primer_trim_2.fastq.gz --out ./

Unicycler version: v0.4.8
Using 2 threads

The output directory already exists and files may be reused or overwritten:
  /home/harshil/repos/nf-core/test/work/56/9196545462ad960685d1c6e132c570

Dependencies:
  Program         Version           Status  
  spades.py       3.13.0            good    
  racon                             not used
  makeblastdb     2.5.0+            good    
  tblastn         2.5.0+            good    
  bowtie2-build   2.4.2             good    
  bowtie2         2.4.2             good    
  samtools        1.11              good    
  java            11.0.8-internal   good    
  pilon           1.23              good    
  bcftools                          not used


SPAdes read error correction (2022-07-11 18:03:05)
    Unicycler uses the SPAdes read error correction module to reduce the number
of errors in the short read before SPAdes assembly. This can make the assembly
faster and simplify the assembly graph structure.

Command: /usr/local/bin/spades.py -1 test/work/56/9196545462ad960685d1c6e132c570/SAMPLE2_PE.primer_trim_1.fastq.gz -2 test/work/56/9196545462ad960685d1c6e132c570/SAMPLE2_PE.primer_trim_2.fastq.gz -o test/work/56/9196545462ad960685d1c6e132c570/spades_assembly/read_correction --threads 2 --only-error-correction
Error: SPAdes crashed! Please view spades.log for more information.

$ cat spades.log

Command line: /usr/local/bin/spades.py  -1      test/work/56/9196545462ad960685d1c6e132c570/SAMPLE2_PE.primer_trim_1.fastq.gz      -2      test/work/56/9196545462ad960685d1c6e132c570/SAMPLE2_PE.primer_trim_2.fastq.gz      -o      test/work/56/9196545462ad960685d1c6e132c570/spades_assembly/read_correction        --threads       2       --only-error-correction

System information:
  SPAdes version: 3.13.0
  Python version: 3.8.6
  OS: Linux-5.10.16.3-microsoft-standard-WSL2-x86_64-with-glibc2.10

Output dir: test/work/56/9196545462ad960685d1c6e132c570/spades_assembly/read_correction
Mode: ONLY read error correction (without assembling)
Debug mode is turned OFF

Dataset parameters:
  Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology or --meta flag if processing metagenomic dataset)
  Reads:
    Library number: 1, library type: paired-end
      orientation: fr
      left reads: ['test/work/56/9196545462ad960685d1c6e132c570/SAMPLE2_PE.primer_trim_1.fastq.gz']
      right reads: ['test/work/56/9196545462ad960685d1c6e132c570/SAMPLE2_PE.primer_trim_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
Other parameters:
  Dir for temp files: test/work/56/9196545462ad960685d1c6e132c570/spades_assembly/read_correction/tmp
  Threads: 2
  Memory limit (in Gb): 15


======= SPAdes pipeline started. Log can be found here: test/work/56/9196545462ad960685d1c6e132c570/spades_assembly/read_correction/spades.log


===== Read error correction started. 


== Running read error correction tool: /usr/local/share/spades-3.13.0-0/bin/spades-hammer test/work/56/9196545462ad960685d1c6e132c570/spades_assembly/read_correction/corrected/configs/config.info

The program was terminated by segmentation fault
=== Stack Trace ===


== Error ==  system call for: "['/usr/local/share/spades-3.13.0-0/bin/spades-hammer', 'test/work/56/9196545462ad960685d1c6e132c570/spades_assembly/read_correction/corrected/configs/config.info']" finished abnormally, err code: -11

In case you have troubles running SPAdes, you can write to [email protected]
or report an issue on our GitHub repository github.com/ablab/spades
Please provide us with params.txt and spades.log files from the output directory.

[josruirod]

Hi, was it resolved? Best

[drpatelh]

Unfortunately not @josruirod. Needs some more digging to figure out what is going on. Quietly hoping someone beats me to it!

[josruirod]

Thanks for answering!