align.seqs: Silva Seed database

Dear,

I’ve got an error running the latest SILVA seed database in align.seqs

mothur > align.seqs(fasta=20160519.trim.contigs.good.unique.fasta, reference=~/Documenten/Silva_Database/V123/silva.seed_v123.align,processors=6)
[ERROR]:  has occurred in the MothurOut class function mothurConvert. Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.

Fortunately my colleague ran into this problem before and he suggested changing the word ‘seed’ in ‘silva.seed_v123.align’ to anything else, made it magically work again. We’ve changed ‘seed’ to ‘seet’ and everything ran perfectly

mothur > align.seqs(fasta=20160519r.trim.contigs.good.unique.fasta, reference=~/Documenten/Silva_Database/V123/silva.seet_v123.align,processors=6)

Using 6 processors.

Reading in the ~/Documenten/Silva_Database/V123/silva.seet_v123.align template sequences...     DONE.
It took 12 to read  14914 sequences.
Aligning sequences from 20160519.trim.contigs.good.unique.fasta ...
It took 10 secs to align 4835 sequences.

Output File Names: 
20160519_sander.trim.contigs.good.unique.align
20160519_sander.trim.contigs.good.unique.align.report

I thought this bug and workaround was worth mentioning.

Kind regards,
Sander

If you run

ls ~/Documenten/Silva_Database/V123/silva*

, what is the output?

 ls ~/Documenten/Silva_Database/V123/silva*
  
/home/swuyts/Documenten/Silva_Database/V123/silva.seed_v123.tax   /home/swuyts/Documenten/Silva_Database/V123/silva.seet_v123.align
/home/swuyts/Documenten/Silva_Database/V123/silva.seet_v123.8mer

Thanks, at some point you must have renamed those files from seed to seet. “seed” won’t work if the file is named “seet”.

Pat

Thanks for your answer Pat.

I think there’s a small misunderstanding here. We had to change the name from ‘seed’ to ‘seet’ in order to make the align.seqs work.

To make it a little bit more clear, I changed ‘~/Documenten/Silva_Database/V123/silva.seet_v123.align’ to ‘~/Documenten/Silva_Database/V123/silva.seed_v123.align’ again and reran the command. Same issue:

# Change name to 'seed' again
mv ~/Documenten/Silva_Database/V123/silva.seet_v123.align ~/Documenten/Silva_Database/V123/silva.seed_v123.align

# run align.seqs
mothur "#align.seqs(fasta=20160519.trim.contigs.good.unique.fasta, reference=~/Documenten/Silva_Database/V123/silva.seed_v123.align,processors=6)"
# Output
mothur > align.seqs(fasta=20160519.trim.contigs.good.unique.fasta, reference=~/Documenten/Silva_Database/V123/silva.seed_v123.align,processors=6)
[ERROR]:  has occurred in the MothurOut class function mothurConvert. Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.

As soon as I change the name again (to anything else this time), the issue is resolved. Here’s the code:

# Change 'silva.seed_v123.align' to anything else
mv ~/Documenten/Silva_Database/V123/silva.seed_v123.align ~/Documenten/Silva_Database/V123/anythingelse.align

# run align.seqs
mothur "#align.seqs(fasta=20160519_sander.trim.contigs.good.unique.fasta, reference=~/Documenten/Silva_Database/V123/anythingelse.align, processors=6)"
# Output
Using 6 processors.

Reading in the ~/Documenten/Silva_Database/V123/anythingelse.align template sequences... DONE.
It took 13 to read  14914 sequences.

Aligning sequences from 20160519_sander.trim.contigs.good.unique.fasta ...
It took 10 secs to align 4835 sequences.


Output File Names: 
20160519_sander.trim.contigs.good.unique.align
20160519_sander.trim.contigs.good.unique.align.report
mothur > quit()

So it only seems to crash when the name is ‘silva.seed_v123.align’, or am I missing something here?

Weird, we haven’t seen this on mac or linux - what operating system and version of mothur are you using?

We’re using Biolinux (based on Ubuntu 14.04) and mothur version 1.36.1.

Apparently this was already previously reported (on Windows) on this forum in the following thread:

When we added the option to seed random in version 1.36, we did not account for “seed” being part of a filename. We have fixed this issue and the change is part of version 1.37 now available, https://github.com/mothur/mothur/releases/tag/v1.37.5.