align-to-tree-mafft-fasttree questions

[MarwaTawfik]

Not sure if that is a bug regarding the constructing the tree in this version (2021.11)?
I worked with that in version qiime2.2021.8 and haven't seen that using the same code.

nice -n 19 qiime phylogeny align-to-tree-mafft-fasttree \
>   --i-sequences dada2-rep-seqs/dada2-rep-seqs.qza \
>   --o-alignment dada2-aligned-rep-seqs.qza \
>   --o-masked-alignment masked-aligned-rep-seqs.qza \
>   --o-tree fasttree-unrooted-tree.qza \
>   --o-rooted-tree fasttree-rooted-tree.qza \
>   --verbose
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: mafft --preservecase --inputorder --thread 1 /tmp/qiime2-archive-nsqe8pwx/875cbcb3-b833-4baf-a147-dd8928e5d635/data/dna-sequences.fasta

inputfile = orig
12712 x 438 - 250 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 ..
 12701 / 12712 (thread    0)
done.

Constructing a UPGMA tree (efffree=0) ...
 12710 / 12712
done.

Progressive alignment 1/2...
STEP   601 / 12711 (thread    0) f
Reallocating..done. *alloclen = 1894
STEP  8601 / 12711 (thread    0) f
Reallocating..done. *alloclen = 3017
STEP  9901 / 12711 (thread    0) f
Reallocating..done. *alloclen = 4700
STEP  10401 / 12711 (thread    0) h
Reallocating..done. *alloclen = 6263
STEP  11301 / 12711 (thread    0) f
Reallocating..done. *alloclen = 8487
STEP  11601 / 12711 (thread    0) f
Reallocating..done. *alloclen = 9829
STEP  12001 / 12711 (thread    0) h
Reallocating..done. *alloclen = 11270
STEP  12301 / 12711 (thread    0) f
Reallocating..done. *alloclen = 12472
STEP  12701 / 12711 (thread    0) f
done.

Making a distance matrix from msa..
 12700 / 12712 (thread    0)
done.

Constructing a UPGMA tree (efffree=1) ...
 12710 / 12712
done.

Progressive alignment 2/2...
STEP  3201 / 12711 (thread    0) f
Reallocating..done. *alloclen = 1894
STEP  8801 / 12711 (thread    0) f
Reallocating..done. *alloclen = 2902
STEP  12301 / 12711 (thread    0) f
Reallocating..done. *alloclen = 3997

Reallocating..done. *alloclen = 5307
STEP  12501 / 12711 (thread    0) f
Reallocating..done. *alloclen = 6350

Reallocating..done. *alloclen = 8277
STEP  12601 / 12711 (thread    0) h
Reallocating..done. *alloclen = 10996
STEP  12701 / 12711 (thread    0) h
done.

disttbfast (nuc) Version 7.490
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-2 (Fast but rough)
 Progressive method (guide trees were built 2 times.)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

[Angela1971]

#1. Making multiple-sequence alignment:
mkdir fast_tree_out
qiime alignment mafft --i-sequences dada2_output/16S-rep-seqs-dada2.qza --p-n-threads 8 --o-alignment fast_tree_out/16S_rep_seqs_mafft.qza

#2. Filtering multiple-sequence alignment:
qiime alignment mask --i-alignment fast_tree_out/16S_rep_seqs_mafft.qza --o-masked-alignment fast_tree_out/16S_rep_seqs_mafft_masked.qza

#3. Running FastTree:
qiime phylogeny fasttree --i-alignment fast_tree_out/16S-rep_seqs_mafft_masked.qza --p-n-threads 8 --o-tree fast_tree_out/16S_rep_seqs_aligned_masked_tree

#4. Make a rooted tree:
qiime phylogeny midpoint-root --i-tree fast_tree_out/16S_rep_seqs_aligned_masked_tree.qza --o-rooted-tree fast_tree_out/16S_rep_seqs_mafft_masked_tree_rooted.qza

[MarwaTawfik]

I did run my above code in qiime2-2021.8 and it worked fine.
nice -n 19 qiime phylogeny align-to-tree-mafft-fasttree
--i-sequences rep-seqs-deblur.qza
--o-alignment aligned-rep-seqs-deblur.qza
--o-masked-alignment masked-aligned-rep-seqs.qza
--o-tree fasttree-unrooted-tree.qza
--o-rooted-tree fasttree-rooted-tree.qza
--verbose
That is why I reported it here.

[Nicholas_Bokulich]

Hi @MarwaTawfik ,
I do not see an error. This just looks like you are seeing the information that mafft reports while running, because you are running in --verbose mode (this is why QIIME 2 has a verbose mode, so that by default you do not see the logging messages that various tools report while they run).

If you get an error message please point it out, otherwise right now it looks like this is probably still just running...

[MarwaTawfik]

thanks very much @Nicholas_Bokulich