Unable to open ..../mothur/lookupFiles/LookUp_Titanium.pat

mothur bugs
1

I downloaded and installed this:

http://www.mothur.org/w/images/8/88/Mothur.cen_64.zip

Trying to run through the 454 SOP. WOrks great until I get to:

mothur > shhh.flows(file=GQY1XT001.flow.files, processors=7)

Unable to open /home/genome/Downloads/mothur/lookupFiles/LookUp_Titanium.pat. Trying mothur’s executable location /home/genome/Downloads/mothur/LookUp_Titanium.pat
Unable to open /home/genome/Downloads/mothur/LookUp_Titanium.pat.

Using 7 processors.
[ERROR]: did not complete shhh.flows.

2

This seems to work

mothur > shhh.flows(file=GQY1XT001.flow.files, processors=7, lookup=./mothur)





Can’t find Lookup in the directory though.


genome@genome-Precision-WorkStation-T5400:~/Downloads$ ls -ltrh total 85M drwxrwxr-x 3 genome genome 4.0K Apr 4 12:39 __MACOSX -rw-r--r-- 1 genome genome 42M May 8 16:30 Mothur.cen_64.zip drwxr-xr-x 3 genome genome 4.0K May 9 15:37 mothur drwxrwxr-x 3 genome genome 4.0K May 9 15:44 longAmpData -rw-r--r-- 1 genome genome 43M May 9 15:48 SOPData.zip drwxrwxr-x 4 genome genome 4.0K May 9 17:07 example-SOP-data -rw-rw-r-- 1 genome genome 54 May 12 21:15 dl.link genome@genome-Precision-WorkStation-T5400:~/Downloads$ find . * | grep LookUp genome@genome-Precision-WorkStation-T5400:~/Downloads$ find . * | grep -i LookUp genome@genome-Precision-WorkStation-T5400:~/Downloads$ du -sh mothur/
3

Can you move the LookUp file to mothur/lookupFIles?

4

That’s the problem. I did a recursive search of all the directories (find . * | grep -i Lookup) and a search via updatedb / locate and I can’t find it in the zip file. It’s like that file doesn’t exist.


genome@genome-Precision-WorkStation-T5400:~/Downloads/example-SOP-data$ sudo updatedb
genome@genome-Precision-WorkStation-T5400:~/Downloads/example-SOP-data$ locate lookup
/home/genome/Desktop/lookupErr
/usr/bin/nmblookup
/usr/bin/nslookup
/usr/lib/perl5/auto/Net/SSLeay/want_X509_lookup.al
/usr/lib/python2.7/dist-packages/ibus/lookuptable.py
/usr/lib/python2.7/dist-packages/ibus/lookuptable.pyc
/usr/lib/python2.7/dist-packages/lxml/pyclasslookup.py
/usr/lib/python2.7/dist-packages/lxml/pyclasslookup.pyc
/usr/lib/python3/dist-packages/lxml/pyclasslookup.py
/usr/lib/python3/dist-packages/lxml/pycache/pyclasslookup.cpython-34.pyc
/usr/lib/python3/dist-packages/mako/lookup.py
/usr/lib/python3/dist-packages/mako/pycache/lookup.cpython-34.pyc
/usr/lib/x86_64-linux-gnu/gedit/plugins/externaltools/filelookup.py
/usr/share/bash-completion/completions/nslookup
/usr/share/foo2zjs/gamma-lookup.ps
/usr/share/man/man1/nmblookup.1.gz
/usr/share/man/man1/nslookup.1.gz
/usr/share/man/man2/lookup_dcookie.2.gz
/usr/src/linux-headers-3.13.0-24-generic/include/config/clkdev/lookup.h

5

ah… got it. dunno how my google foo missed it before. using the wiki search engine???

http://www.mothur.org/wiki/Lookup_files