MAFFT alignment error when running nextstrain snakemake file

Question

[laxvid]

I get an error while aligning sequences using the nextstrain snakemake file It simply says:

ERROR: b''

Any pointers to what may be happening will be appreciated -Lax

[Mon Apr 27 14:12:43 2020]
Job 29:
        Aligning sequences to config/reference.gb
          - gaps relative to reference are considered real
        Cluster:  11



ERROR: b''
shell exited 1 when running: mafft --reorder --anysymbol --nomemsave --adjustdirection --thread 2 results/split_alignments/11.fasta.to_align.fasta 1> results/split_alignments/11.fasta 2> results/split_alignments/11.fasta.log

[Mensur Dlakic]

Not a bash expert, but to me this seems like an error in redirection. I suggest you check if you can run either of these two commands outside of your pipeline:

mafft --reorder --anysymbol --nomemsave --adjustdirection --thread 2 results/split_alignments/11.fasta.to_align.fasta
mafft --reorder --anysymbol --nomemsave --adjustdirection --thread 2 results/split_alignments/11.fasta.to_align.fasta > results/split_alignments/11.fasta

If either of them works, it is likely that splitting the stdout and stderr outputs is causing the problem.

Answer 1

[fkfikrikarim]

One problem that cause this error is I had some formatting issue with the sequences.fasta

TAATTTTAGTAGTGC>Japan/Hu_DP_Kng_19-027/2020

Check your fasta again and see whether it solves the issue.

I got that formatting problem because I use cat to merge two separate fasta files without adding new line first.