sequences dropped during alignment

[NikitaSitharam]

Hi there,

I have tried to align 1084 Clade I mpox sequences using Squirrel. However, eight sequences were dropped during alignment without any error message (KP739434.1, KP739437.1, KP739439.1, KP739442.1, KP739444.1, KP739447.1, JF792045.1, JF799095.1). Six of these sequences are ~2600 bp and two are 961 bp. These sequences were not present in any of the output files.

Please see the output from the terminal:

squirrel clade_i.fasta --clade cladei -qc --outdir squirrel/first_run/
Query file: clade_i.fasta
QC mode activated. Squirrel will flag:

• Clumps of unique SNPs
• SNPs adjacent to Ns
• Sequences with high N content
  60 sequences flagged as high N content (>0.2): suggested_to_exclude.csv
  Building DAG of jobs...
  Using shell: /bin/bash
  Provided cores: 1 (use --cores to define parallelism)
  Rules claiming more threads will be scaled down.
  Job stats:
  job count

---

align_to_reference 1
all 1
mask_repetitive_regions 1
total 3

Select jobs to execute...
Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Select jobs to execute...
Select jobs to execute...
Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Select jobs to execute...
1176 masked, aligned sequences written to: clade_i.aln.fasta
Select jobs to execute...
Complete log: .snakemake/log/2025-05-20T095503.681980.snakemake.log
Number of possibly problematic SNPs: 441
Flagged mutations writted to: clade_i.suggested_mask.csv
Generating: clade_i.report.html

[aineniamh]

Thanks for flagging this, squirrel is primarily designed to align and analyse whole genome data, however it should report when sequences get dropped. I'll put a note to add this in as a warning.