MAFFT alignment error when running nextstrain snakemake file
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
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fkfikrikarim •
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laxvid •
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laxvid •
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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.
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Not a
bashexpert, 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:If either of them works, it is likely that splitting the
stdoutandstderroutputs is causing the problem.