Using mothur examples as is runs into problems...

Commands in mothur
1

Hi all,

I’m just beginning to look at mothur and I have been running into some problems -

  1. The example (Costello stool analysis) documentation has many problems in the illustrated outputs. I realize they are only illustrations, but using the data downloaded I have been getting slightly different results. Is this normal? Also, the number of good filtered sequences after 6 or 7 steps does not seem to be what the output box says…is that because I’m running on Linux? Also, I got different results on two different runs (16 once and 2 next time) for the final good and unique sequences. Is this normal?

  2. I am trying to run the modified version of chimaera slayer, but it expects blast executables somewhere in the installed mothur tree and I am not sure where to get the executables - formatdb, blastall, and megablast. Here are the errors -

mothur > chimera.slayer(reference=silva.gold.align, processors=2)

Using stool.trim.unique.good.align as input file for the fasta parameter.
Checking sequences from stool.trim.unique.good.align …
Reading sequences from silva.gold.align…Done.
[ERROR]: /largefs/aragam/Mothur-1.19.4/blast/bin/formatdb file does not exist. mothur requires formatdb.exe to be in the ./blast/bin folder relative to the mothur.exe location.
[ERROR]: /largefs/aragam/Mothur-1.19.4/blast/bin/blastall file does not exist. mothur requires blastall.exe to be in the ./blast/bin folder relative to the mothur.exe location.
[ERROR]: /largefs/aragam/Mothur-1.19.4/blast/bin/megablast file does not exist. mothur requires megablast.exe to be in the ./blast/bin folder relative to the mothur.exe location.

Could someone please help me? I am very very new to mothur and the sequencing software. Thanks much in advance,

Nash

2

Hi Naragam,

For the first problem, I’ve also see this using the downloaded data, and don’t know why. For the second one, I fixed it just copy the executable formatdb, blastall, megablast under the folder requaired. You can have a try!

3

Hi

If you are running Mothur on a Linux-based server, I’d assume your system already has formatdb, blastall and megablast installed.

Use “which” command to find out where these files located on your server, e.g, formatdb on my server is located at /opt/binfo/blast/bin/formatdb,
Use “cp” command to copy these files to mothur/Mothur.source/blast/bin

[b]$which formatdb blastall megablast
/opt/binfo/blast/bin/formatdb
/opt/binfo/blast/bin/blastall
/opt/binfo/blast/bin/megablast

$cp cp /opt/binfo/blast/bin/formatdb /opt/binfo/blast/bin/blastall /opt/binfo/blast/bin/megablast mothur/Mothur.source/blast/bin[/b]

Now run the chimera.slayer in Mothur, you should be fine.

It won’t work if you copied those Windows-based executable files (extension as .exe) to the folder, just keep that in mind.

Hope this helps.