build a phylogenetic tree

Dear all,

I run the workflow as described in QIIME 2 tutorial to perform analysis of microbiome data generated by NGS technology. After achieving taxonomy classification step with success i’m trying to build phylogenetic tree. To perform sequence alignement i run this command
qiime alignment mafft
–i-sequences rep-seqs.qza
–p-parttree
–o-alignment aligned-rep-seqs.qza
Noting that i used rep-seqs.qza file generated after clustering by VSEARCH method because to perform this task featuredata [sequence] file is required instead of featuredata [taxonomy].
After running the aforementioned command i received this message :
Plugin error from alignment:
Command ‘[‘mafft’, ‘–preservecase’, ‘–inputorder’, ‘–thread’, ‘1’, ‘–parttree’, ‘/tmp/qiime2-archive-mdoea5qz/65ebb549-31b5-4f24-8ef3-958428774fc9/data/dna-sequences.fasta’]’ returned non-zero exit status 1.
I need your help to resolve this problem.

Hi @M_F,

Hopefully, we can help.

Which tutorial? Have you read through the q2-phylogeny tutorial? More details and options can be found here.

Can you clarify this? Are you running this command on your own data, or trying to run through one of the QIIME tutorials? If so, which one? Also, is there a reason why you are using --p-parttree? This is not required unless you have more than 1,000,000 representative sequences to align.

Can you can try re-running the command with the --verbose option? This will allow you to see the on-screen output from mafft, and may help to track down what the issue is.

-Best wishes!
-Mike

Dear Mike,

Thank you for the message.
I read the tutorial https://docs.qiime2.org/2020.2/tutorials/phylogeny/. In order to build the phylogenetic tree i need to perform alignment of sequences using MAFFT and i used -p–parttree option because i have more than 1,000,000 representative sequences to align. I will try the --verbose option as you recommended to see the output from mafft.
Best regards

1 Like

Hello @SoilRotifer,

i tried the alignment using MAFFT and i used the --verbose option i obtained the error message :
subprocess.CalledProcessError: Command ‘[‘mafft’, ‘–preservecase’, ‘–inputorder’, ‘–thread’, ‘1’, ‘–parttree’, ‘/tmp/qiime2-archive-d7y6omai/65ebb549-31b5-4f24-8ef3-958428774fc9/data/dna-sequences.fasta’]’ returned non-zero exit status 1. m
Alignment 7-3 m
Plugin error from alignment:

Command ‘[‘mafft’, ‘–preservecase’, ‘–inputorder’, ‘–thread’, ‘1’, ‘–parttree’, ‘/tmp/qiime2-archive-d7y6omai/65ebb549-31b5-4f24-8ef3-958428774fc9/data/dna-sequences.fasta’]’ returned non-zero exit status 1.

See above for debug info.
How can i resolve the problem ?

Hi @M_F,

I just realized that this issue cropped up before, and often implies there is not enough memory available on your system, and/or there are too-many ambiguous / gappy sites in your data.

-Mike