align.seqs: Silva Seed database

mothur bugs
1

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

2

If you run

ls ~/Documenten/Silva_Database/V123/silva*

, what is the output?

3 
 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
4

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

5

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?

6

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

7

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:
http://mothur.ltcmp.net/t/problem-bug-with-align-seqs/2567/1

8

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.