As I was making my way through the Costello tutorial, I cannot get chimera.slayer command to work although I have downloaded the file:blast-2.2.16-universal-macosx.tar.gz from the website and followed the directions on the chimera wiki page. I placed both the formatdb and megablast executables in a folder I call blast/bin and placed this folder beside the mother executable in my mothurtutorial folder located on my desktop. This is the output:
mothur > chimera.slayer(reference=silva.gold.align, processors=4)
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.
sh: ./blast/bin/formatdb: No such file or directory
Only reporting sequence supported by 90% of bootstrapped results.
sh: ./blast/bin/megablast: No such file or directory
sh: ./blast/bin/megablast: No such file or directory
sh: ./blast/bin/megablast: No such file or directory
sh: ./blast/bin/megablast: No such file or directory
I am very new to the mac world so please tell me what am I doing wrong?
Thank you
We’re working on a far less wonky fix for this and apologize for the problems people are having. When you go into your “mothurtutorial” folder and type “ls” do you see an executable file called “mothur” and a folder called “blast”?
Pat
If I type “Is” when I click on the folder mothurmanual, I see the mother executable and a folder named “blast/bin” that I created, but not a folder named “blast”. When I downloaded the 2.2.16 file, I created a folder named blast/bin and dragged the blast and formatdb executable files from the bin folder (from the downloaded file) into the blast/bin folder that I created. Otherwise, If I type “Is” in the search window after I click on the folder mothermanual I see neither the mothur executable or the blast/bin folder I created.?
sorry - too much shorthand… next to the executable should be a folder called blast. inside the folder called blast should be a folder called bin. inside that folder should be a number of executables including formatdb and megablast
Yes. The folder “blast-2.2.16” is next to the mothur executable and within that folder is the “bin” folder which contains the executables. I created a folder titled “blast/bin” and dragged the formatdb and megablast executables into the blast/bin folder from their original bin folder. I then placed both the blast/bin and blast-2.2.16 folders into my mothurtutorial folder.
can you post the output of typing the following (starting inside of mothurmanual)…
ls
cd blast
ls
cd bin
ls
d-ip-10-195-51-223:desktop kd$ cd mothurmanual
d-ip-10-195-51-223:mothurmanual kd$ ls
Other stuff stool.scrap.qual
Skip chimera slayer stool.trim.fasta
blast stool.trim.fasta.summary
mothur stool.trim.good.names
mothur.1305138030.logfile stool.trim.names
mothur.1305234848.logfile stool.trim.qual
silva.bacteria.8mer stool.trim.unique.align
silva.bacteria.fasta stool.trim.unique.align.report
silva.gold.align stool.trim.unique.align.summary
stool.fasta stool.trim.unique.bad.accnos
stool.fasta.summary stool.trim.unique.fasta
stool.good.groups stool.trim.unique.fasta.summary
stool.groups stool.trim.unique.good.align
stool.oligos stool.trim.unique.good.align.summary
stool.qual trainset6_032010.rdp.fasta
stool.scrap.fasta trainset6_032010.rdp.tax
d-ip-10-195-51-223:mothurmanual kd$ cd blast
d-ip-10-195-51-223:blast kd$ ls
VERSION bin data doc
d-ip-10-195-51-223:blast kd$ cd bin
d-ip-10-195-51-223:bin kd$ ls
bl2seq blastpgp formatdb makemat seedtop
blastall copymat formatrpsdb megablast
blastclust fastacmd impala rpsblast
d-ip-10-195-51-223:bin kd$ quit()
It looks like you have things in the right place. What error are you getting now?
Looks similar to the first error message:
mothur > set.current(fasta=stool.trim.unique.good.align, name=stool.trim.good.names)
Current files saved by mothur:
fasta=stool.trim.unique.good.align
name=stool.trim.good.names
mothur > chimera.slayer(reference=silva.gold.align, processors=4)
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.
sh: /bin/blast/bin/formatdb: No such file or directory
Only reporting sequence supported by 90% of bootstrapped results.
sh: /bin/blast/bin/megablast: No such file or directory
sh: /bin/blast/bin/megablast: No such file or directory
sh: /bin/blast/bin/megablast: No such file or directory
sh: /bin/blast/bin/megablast: No such file or directory
Thanks
Athenia Oldham
Athenia,
Something has changed - mothur is now looking in /bin/blast/bin/ for the executables instead of ./blast/bin/. Did you modify the source code or change how you’re running mothur?
Pat
When I first downloaded mothur onto my new mac computer, a student typed the following into the terminal “sudo cp mothur /bin” telling me that I would be able to access mothur from anywhere on my computer and it has been that way this whole time (as we did not know how to undo this command). The only thing that I have changed since my first post was instead of creating a new folder named “blast/bin” and dragging the two executables from the downloaded blast2.2.16 folder into it was to change the name of the downloaded blast2.2.16 folder to “blast” and placing that in my mothurmanual folder by the mothur executable.
I am not sure if I changed the source code.
Is there a way to undo the “sudo cp mothur /bin” command?
Thank you for your continued help with this issue
Athenia Oldham
It sounds like you probably have mothur in two places and aren’t necessarily using the one you intend - could you type the following at the prompt?
which mothur
and let us know what you get back?
pat
Last login: Wed May 18 08:26:14 on console
d-ip-10-195-51-223:~ kd$ which mothur
/bin/mothur
d-ip-10-195-51-223:~ kd$