I am trying to align some sequences following the steps given in the “Moving pictures” tutorial to create a phylogenetic tree; I am using :
**$ qiime alignment mafft **
**–i-sequences rawmilk_rep-seqs.qza **
Apparently everything is correct, but then appears the next error:
Plugin error from alignment:
** Command ‘[‘mafft’, ‘–preservecase’, ‘–inputorder’, ‘–thread’, ‘1’, ‘/scratch/summit/
[email protected]/tmp/qiime2-archive-xy8gexli/874deeab-85ae-48de-bcc1-5b091bd39378/data/dna-sequences.fasta’]’ returned non-zero exit status 1**
Debug info has been saved to /scratch/summit/ [email protected]/tmp/qiime2-q2cli-err-uhpsdoaj.log
I tried to get more information with the
verbose command, but the error is still the same, I did not get more information available.
What is exactly the error? What Does it mean? How can I fix it?
Thanks for your assistance.
Sorry to hear about your trouble.
Could you share with your
rawmilk_rep-seqs.qza and, if possible, the log file?
Hi Antonio, thanks, here is it
rawmilk_rep-seqs.qza (1.8 MB)
I hope this work.
It looks like this is an old trouble, maybe related to memory or an internal process in mafft, as observed here:
Hi, I’m experiencing the same issue. Here is the error message:
qiime alignment mafft --i-sequences uchime-dn-out/rep-seqs-nonchimeric-dn.qza --p-n-threads 12 --output-dir alignment_out --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 12 /tmp/qiime2-archive-ufn…
@gilberto_solano - I am glad you found that post - I agree with your assessment. Is there a machine with more memory you could run this on? Alternatively, you could check out q2-fragment-insertion for an alternative method for building a tree.
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