raxml erroring out with `skip_samples` param

[sateeshperi]

Describe the bug

Error executing process > 'NFCORE_MYCOSNP:MYCOSNP:CREATE_PHYLOGENY:RAXMLNG (1)'

Caused by:
  Process `NFCORE_MYCOSNP:MYCOSNP:CREATE_PHYLOGENY:RAXMLNG (1)` terminated with an error exit status (1)

Command executed:

  raxml-ng \
      --all --model GTR+G --bs-trees 1000 \
      --msa combined_vcf-to-fasta.fasta \
      --threads 2 \
      --prefix output

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_MYCOSNP:MYCOSNP:CREATE_PHYLOGENY:RAXMLNG":
      raxmlng: $(echo $(raxml-ng --version 2>&1) | sed 's/^.*RAxML-NG v. //; s/released.*$//')
  END_VERSIONS

Command exit status:
  1

Command output:

  RAxML-NG v. 1.0.3 released on 21.07.2021 by The Exelixis Lab.
  Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
  Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
  Latest version: https://github.com/amkozlov/raxml-ng
  Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

  System: Intel(R) Xeon(R) Gold 5215 CPU @ 2.50GHz, 4 cores, 7 GB RAM

  RAxML-NG was called at 09-Mar-2022 18:44:28 as follows:

  raxml-ng --all --model GTR+G --bs-trees 1000 --msa combined_vcf-to-fasta.fasta --threads 2 --prefix output

  Analysis options:
    run mode: ML tree search + bootstrapping (Felsenstein Bootstrap)
    start tree(s): random (10) + parsimony (10)
    bootstrap replicates: 1000
    random seed: 1646869468
    tip-inner: OFF
    pattern compression: ON
    per-rate scalers: OFF
    site repeats: ON
    branch lengths: proportional (ML estimate, algorithm: NR-FAST)
    SIMD kernels: AVX
    parallelization: coarse-grained (auto), PTHREADS (2 threads), thread pinning: OFF

  [00:00:00] Reading alignment from file: combined_vcf-to-fasta.fasta
  [00:00:00] Loaded alignment with 3 taxa and 45 sites

  ERROR: Your alignment contains less than 4 sequences! 

  ERROR: Alignment check failed (see details above)!

Command wrapper:

  RAxML-NG v. 1.0.3 released on 21.07.2021 by The Exelixis Lab.
  Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
  Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
  Latest version: https://github.com/amkozlov/raxml-ng
  Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

  System: Intel(R) Xeon(R) Gold 5215 CPU @ 2.50GHz, 4 cores, 7 GB RAM

  RAxML-NG was called at 09-Mar-2022 18:44:28 as follows:

  raxml-ng --all --model GTR+G --bs-trees 1000 --msa combined_vcf-to-fasta.fasta --threads 2 --prefix output

  Analysis options:
    run mode: ML tree search + bootstrapping (Felsenstein Bootstrap)
    start tree(s): random (10) + parsimony (10)
    bootstrap replicates: 1000
    random seed: 1646869468
    tip-inner: OFF
    pattern compression: ON
    per-rate scalers: OFF
    site repeats: ON
    branch lengths: proportional (ML estimate, algorithm: NR-FAST)
    SIMD kernels: AVX
    parallelization: coarse-grained (auto), PTHREADS (2 threads), thread pinning: OFF

  [00:00:00] Reading alignment from file: combined_vcf-to-fasta.fasta
  [00:00:00] Loaded alignment with 3 taxa and 45 sites

  ERROR: Your alignment contains less than 4 sequences! 

  ERROR: Alignment check failed (see details above)!

Work dir:
  /mycosnp-nf/work/b3/8cb204c43b712f83738a16d8ed3b6a

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

Impact

To Reproduce Steps to reproduce the behavior: nextflow run main.nf -profile singularity,test --skip_samples ERR2172266 -resume

[sateeshperi]

wonder why it wasn't just ignored as is the error strategy?

[mciprianoCDC]

When I run this it gives same error but full workflow still completes. Take that back, it doesn't run multiqc.

[mciprianoCDC]

To Fix: Run raxmlng only if number of sequences >=3 Run iqtree only if number of sequences >=3