Hello,
I am working on mpox surveillance in Thailand.I initially attempted to run the mpox Nextstrain analysis on my local notebook using the default settings because I don’t yet have access to AWS S3. However, I encountered an error.
kritchy@Kritchys-MacBook-Pro mpox % nextstrain build . --configfiles defaults/config.yaml
Error: no Snakefile found, tried Snakefile, snakefile, workflow/Snakefile, workflow/snakefile.
I also attempted to run the Augur pipeline, but encountered an error that I believe may be related to insufficient memory.
Could you give me suggestions on how to contribute to Nextstrain’s mpox analysis in Thailand? Also, how many whole-genome mpox FASTA files can typically be run on a local notebook?
/usr/local/bin/mafft: line 2747: 269 Killed “$prefix/disttbfast” -q $npickup -E $cycledisttbfast -V “-”$gopdist -s $unalignlevel $legacygapopt $mergearg -W $tuplesize $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreads-$numthreadstb $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -g $gexp -f “-”$gop -Q $spfactor -h $aof $param_fft $algopt $treealg $scoreoutarg $anchoropt -x $maxanchorseparation $oneiterationopt < infile > pre 2>> “$progressfile”
e = orig
subalignment = 0
subalignmentoffset = 0
5 x 197209 - 660 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
generating a scoring matrix for nucleotide (dist=200) … done
Gap Penalty = -1.53, +0.00, +0.00
Making a distance matrix …
There are 37085 ambiguous characters.
1 / 5 (thread0)
done.
Constructing a UPGMA tree (efffree=0) …
0 / 5
done.
Progressive alignment 1/2…
STEP 1 / 4 (thread 0) f
STEP2 / 4 (thread 0) f