Hi, @trs.
I am having a similar problem:
> Error in rule align:
> jobid: 22
> output: results/aligned.fasta
> log: logs/align.txt (check log file(s) for error message)
> shell:
>
> mafft --auto --thread 10 --keeplength --addfragments results/prefiltered.fasta defaults/reference_seq.fasta > results/aligned.fasta 2> logs/align.txt
>
> (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
> Logfile logs/align.txt:
> nadd = 424033
> npair = 424033
> nseq = 424034
> nlen = 34692
> use ktuples, size=6!
> nadd = 424033
> ppenalty_ex = -10
> nthread = 10
> blosum 62 / kimura 200
> sueff_global = 0.100000
> norg = 1
> njobc = 2
> generating a scoring matrix for nucleotide (dist=200) ... done
>
>
> Making a distance matrix ..
> /home/fernando_hayashi/miniconda3/envs/nextstrain/bin/mafft: line 2747: 35443 Killed "$prefix/addsingle" -Q 100 $legacygapopt -W $tuplesize -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>> "$progressfile"
>
>
> Removing output files of failed job align since they might be corrupted:
> results/aligned.fasta
> Shutting down, this might take some time.
> Exiting because a job execution failed. Look above for error message
> Complete log: /home/fernando_hayashi/Documentos/sars-cov-2/ncov/.snakemake/log/2021-01-29T092954.195478.snakemake.log
Do you think it is a RAM problem? I am running my analysis on a Intel® Xeon® W-2235 CPU @ 3.80GHz × 12 (64GB of RAM). Because of this problem I asked about the minimum specs for using nextstrain, and you answered that my computer was fine for it.