shhh.flows can't find necessary file?

I decided to give the command a whirl on a 32-bit Windows 7 PC that would otherwise be sitting disgracefully idle all weekend anyway. I started the command running last night and when I checked in this morning, this is what I found - everything ran fine until the shhh.flows command couldn’t find a file called “lookup_titanium.pat”.

mothur v.1.22.1
Last updated: 10/24/2011

by
Patrick D. Schloss

Department of Microbiology & Immunology
University of Michigan
pschloss@umich.edu
http://www.mothur.org

When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, co
mmunity-supported software for describing and comparing microbial communities. A
ppl Environ Microbiol, 2009. 75(23):7537-41.

Distributed under the GNU General Public License

Type 'help()' for information on the commands that are available

Type 'quit()' to exit program



mothur > set.dir(tempdefault=C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.s
hhh.flows)

Mothur's directories:
tempDefault=C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\

mothur > sffinfo(sff=Region1.APT.sff, flow=T)

Unable to open Region1.APT.sff. Trying default C:\Users\Jo\Documents\Mothur\Anal
ysis\Region1.APT.shhh.flows\Region1.APT.sff
Extracting info from C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flow
s\Region1.APT.sff ...
10000
20000
30000
40000
50000
60000
70000
80000
90000
100000
110000
114250
It took 332 secs to extract 114250.
Output File Names:
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.fasta
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.qual
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.flow


mothur > trim.flows(flow=Region1.APT.flow, oligos=10-2010.oligos, pdiffs=2, bdif
fs=1, processors=2)

Unable to open Region1.APT.flow. Trying default C:\Users\Jo\Documents\Mothur\Ana
lysis\Region1.APT.shhh.flows\Region1.APT.flow
Unable to open 10-2010.oligos. Trying default C:\Users\Jo\Documents\Mothur\Analy
sis\Region1.APT.shhh.flows\10-2010.oligos
10000
20000
30000
40000
50000
60000
70000
80000
90000
100000
110000
114250

Output File Names:
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.trim.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.scrap.f
low
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9410.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9412.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9413.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9414.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9415.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9416.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9417.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9418.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9419.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9420.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9425.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9426.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9427.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9428.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9429.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9430.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9431.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9432.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9433.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9434.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9435.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9436.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9437.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9438.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9440.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9442.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9443.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9447.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9449.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9450.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9451.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9452.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9453.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9454.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9455.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9459.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9462.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9463.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9464.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9465.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9466.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9467.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9468.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9469.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9470.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9471.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9472.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9473.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9474.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.9475.fl
ow
C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Region1.APT.flow.fi
les


mothur > shhh.flows(file=Region1.APT.flow.files, processors=2)

Unable to open Region1.APT.flow.files. Trying default C:\Users\Jo\Documents\Moth
ur\Analysis\Region1.APT.shhh.flows\Region1.APT.flow.files
Unable to open LookUp_Titanium.pat. Trying default C:\Users\Jo\Documents\Mothur\
Analysis\Region1.APT.shhh.flows\LookUp_Titanium.pat
Unable to open C:\Users\Jo\Documents\Mothur\Analysis\Region1.APT.shhh.flows\Look
Up_Titanium.pat. Trying mothur's executable location C:\Users\Jo\Documents\Mothu
r\Program Files\LookUp_Titanium.pat
Unable to open C:\Users\Jo\Documents\Mothur\Program Files\LookUp_Titanium.pat.

I have no idea what this file is - presumably something that should have been bundled in the windows executable but the program can’t find it?

You need to copy the file LookUp_Titanium.pat from the source directory into the directory where you have your executable (that is, if you compiled from source), or perhaps in the directory where you started mothur. Also copy the GSFLX and GS20 files if you are using those chemistries. I imagine these files are included with the binary distribution, but I’m not sure.

I actually had to rename the file mothurLookUp_Titanium.pat in order to get it to work with the mpi version when I put the file in the directory with the binary (slight bug there?)

“Unable to open LookUp_Titanium.pat. Trying mothur’s executable location /share/apps/mothur/mothurLookUp_Titanium.pat”

Bob

I see now that the file is provided as a separate download from the wiki here http://www.mothur.org/wiki/Lookup_files. I don’t know how I missed it when reading about shhh.flows, and then when I searched the wiki I was using the full file name and getting no hits. Thank you for the help.

Bob,
It looks like mothur may to getting the path mothur’s executable location wrong when it is looking for the Lookup file. I am not able to reproduce it on my machine, but is mothur’s executable path /share/apps/mothur/mothur or /share/apps/mothur?
-Sarah

Sarah:

Haven’t been on lately because I’ve been reinstalling my computer (changed to a larger HD). Now back to my mothur analysis!

The executable location directory is /share/apps/mothur, the direct path to the executables are /share/apps/mothur/mothurMPI and /share/apps/mothur/mothur (the exe’s are in the mothur folder.

Bob

Hi,

not to hijack this topic, but I was wondering if mothur ‘knows’ which lookup file has to be used, or do you have to set it manually? If I don’t include the titanium file it gives an error (we used a GS FLX).

thanks

regards,
Kirk

The default is the Titanium file. You would need to change the file using the lookup option in shhh.flows. You can get the files here…

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

How are you running the command and what’s the error you’re getting?

Hi,

I am having the same issue with mothur not being able to find the GSFLX lookup file even if I specify it with the lookup option? Using 1.24.1 (I would update to 1.25 but this is a bit of a pain since it’s a cluster computing setup and getting them to update is a real rigmarole!)

The lookup file is in the same directory as the data.

Also what are the default min/max flows paramters for GSFLX in mothur? or does it have 450 from titanium? If it is 450 what are the recommended for gs flx? I saw on the quince paper that the max he uses is 360 but not sure on the min.

Cheers,
Tris

Have you tried to just put the LookUp file into the directory with your data?

We don’t have a good handle on what to set min/maxflows to for GSFLX. Unfortunately, a lot of the mock community data out there looks pretty crappy when we try adjusting the number of flows. I’d probably set minflows=250, maxflows=250. Again, that’s an educated guess.

Hi,
How could I change the default parameter for LookUp when running shhh.flow? Mothur is looking for LookUpTitanium and what I have into my directory, with my data, is the Lookup GSFLX?

Thanks,
Cristina

Have you tried using the lookup option?

Thanks!

Worked beutifully adding the option lookup

shhh.flows(file=nameofthefile, lookup=LookUp_GSFLX.pat)

Hi Pat,

Weird, I just used lookup=Lookup_GSFLX.pat and it worked but when I put the whole path to the lookup file it keeps saying

mothur > shhh.flows(file=study_sample.flow.files, lookup=/share/scratch/z3265008/sample_data/LookUp_GSFLX.pat, processors=8)
Unable to open /share/scratch/z3265008/sample_data/LookUp_GSFLX.pat
Unable to open /share/scratch/z3265008/sample_data/LookUp_GSFLX.pat. Trying mothur’s executable location /share/apps/mothur/1.24.1/bin//share/scratch/z3265008/sample_data/LookUp_GSFLX.pat
Unable to open /share/apps/mothur/1.24.1/bin//share/scratch/z3265008/sample_data/LookUp_GSFLX.pat.

Oh well, at least it’s doing it!
Thanks,
Tris

Sometimes the lookUp file is in the same folder as your data and the executable mothur file as well, but still you see this error “Unable to open LookUp_Titanium.pat , Trying mothur’s executable location”

I tried the following command and the error was gone

mothur > shhh.flows(file=/mothur/yourfilename.flow.files, lookup=/mothur, processors=8)

***my files are all saved in the folder named “mothur” which is located in the root

hope this helps

Hi all,

I am facing the same problem:

mothur > shhh.flows(file=/host/Full_plate_11_07_2013/half1st_analysis/ICHK6WT01.flow.files, lookup=LookUp_GSFLX.pat)

Unable to open /media/trl835/OSDisk/Full_plate_11_07_2013/ICHK6WT01.MID67.flow. Trying mothur’s executable location /host/mothur/mothur/ICHK6WT01.MID67.flow
Unable to open /host/mothur/mothur/ICHK6WT01.MID67.flow. Disregarding.
Unable to open /media/trl835/OSDisk/Full_plate_11_07_2013/ICHK6WT01.MID68.flow. Trying mothur’s executable location /host/mothur/mothur/ICHK6WT01.MID68.flow
Unable to open /host/mothur/mothur/ICHK6WT01.MID68.flow. Disregarding.
Unable to open /media/trl835/OSDisk/Full_plate_11_07_2013/ICHK6WT01.MID69.flow. Trying mothur’s executable location /host/mothur/mothur/ICHK6WT01.MID69.flow
Unable to open /host/mothur/mothur/ICHK6WT01.MID69.flow. Disregarding.
Unable to open /media/trl835/OSDisk/Full_plate_11_07_2013/ICHK6WT01.MID70.flow. Trying mothur’s executable location /host/mothur/mothur/ICHK6WT01.MID70.flow
Unable to open /host/mothur/mothur/ICHK6WT01.MID70.flow. Disregarding.
Unable to open /media/trl835/OSDisk/Full_plate_11_07_2013/ICHK6WT01.MID71.flow. Trying mothur’s executable location /host/mothur/mothur/ICHK6WT01.MID71.flow
Unable to open /host/mothur/mothur/ICHK6WT01.MID71.flow. Disregarding.
Unable to open /media/trl835/OSDisk/Full_plate_11_07_2013/ICHK6WT01.MID72.flow. Trying mothur’s executable location /host/mothur/mothur/ICHK6WT01.MID72.flow
Unable to open /host/mothur/mothur/ICHK6WT01.MID72.flow. Disregarding.
Unable to open /media/trl835/OSDisk/Full_plate_11_07_2013/ICHK6WT01.MID73.flow. Trying mothur’s executable location /host/mothur/mothur/ICHK6WT01.MID73.flow
Unable to open /host/mothur/mothur/ICHK6WT01.MID73.flow. Disregarding.
Unable to open /media/trl835/OSDisk/Full_plate_11_07_2013/ICHK6WT01.MID74.flow. Trying mothur’s executable location /host/mothur/mothur/ICHK6WT01.MID74.flow
Unable to open /host/mothur/mothur/ICHK6WT01.MID74.flow. Disregarding.
Unable to open /media/trl835/OSDisk/Full_plate_11_07_2013/ICHK6WT01.MID75.flow. Trying mothur’s executable location /host/mothur/mothur/ICHK6WT01.MID75.flow
Unable to open /host/mothur/mothur/ICHK6WT01.MID75.flow. Disregarding.
Unable to open /media/trl835/OSDisk/Full_plate_11_07_2013/ICHK6WT01.MID76.flow. Trying mothur’s executable location /host/mothur/mothur/ICHK6WT01.MID76.flow
Unable to open /host/mothur/mothur/ICHK6WT01.MID76.flow. Disregarding.
[ERROR]: no valid files.

Using 4 processors.

I have tried both Titanium and GSFLX lookup files with different locations! Did not work. anybody knows whats wrong please?

The error you are getting is referring to the flow files listed in the file option, not the lookup file. Can you try giving the full path to the flow files in the file? What version of mothur are you running?

Thanks for replying, the path mentioned above is my flow.files full path, or at least this is what I think Do you think it should be different!? and I am using mothur mothur v.1.27.0

I have tried installing newer versions of mothur but it keeps bouncing back unable to be installed on my PC, it kept asking for libraries depencines or some sort of stuff that I couldnt manage get around it so I sticked to this version. I have QIIME installed as well if this could be a reason (just me being very naive assuming), am not a proper bioinformatician you can tell

I would recommend upgrading to our current version, 1.31. I suspect that will resolve the issue you are having. It also includes many new commands, feature updates and bug fixes. What OS are you running mothur on? Could you post the install error you are getting?

I removed mothur and tried to re install it, it gave me the same problem. the error is:
./mothur: error while loading shared libraries: libreadline.so.5: cannot open shared object file: No such file or directory

I tried the command:
sudo apt-get install libreadline-dev libreadline5-dev

but did not resolve it unfortunately. I am using Ubuntu 12.10 64-bit

Here’s a link to a forum post by a user with a similar issue with the readline libraries, Error in readline installing new He was able to resolve the issue and I hope it will be helpful to you. The other option you have is to download the version of mothur for Linux without readline, http://www.mothur.org/wiki/Download_mothur#Linux_executable.