ERROR: data file not found: riss_COI_genbank_pisinna_aln.nex!

[Lara Baptista]

Hi!

I'm using Garli 2.0 on XSEDE in CIPRES Gateway for the first time, in an attempt to run an analysis with partitioned data under different models. I haven't been able to perform any analysis so far because I keep retrieving messages with Errors. The first time I tried to run it, I had troubles with the definition of the models and partitions but after looking in the forum I finally found out my problem. 

Now I keep getting the "ERROR: data file not found: riss_COI_genbank_pisinna_aln.nex!" when I submit the job to the CIPRES server. I already created a new configuration file using the GARLI.conf Creator tool, but I keep getting this problem. The job is submitted and I get some output files, namely files "COI_pisinna_bs1.run13.screen.log", but all of them present the message with the error and no results. The NEXUS file is saved in the Data Folder at CIPRES. Can this problem be associated with the maximum hours defined to run the proccess (I get the output files and receive the email informing the job is done long before the maximum time is reached)?

The NEXUS and configuration files are attached.

Thank you,

LBaptista

[Derrick Zwickl]

Hi Lara,

Sorry for my slow reply.  I don't have any direct connection to the CIPRES portal, so I don't know if I can help much with your problem.

I don't think that the problem is with the settings in your configuration file.  I can get your files to run fine on my laptop.  It looks like when the program is started it immediately cannot find the alignment file and stops. 

My guess would be that the alignment isn't being properly copied to the correct directory by the portal.  So, if you haven't already, I would just try again.  If that fails, contact portal support.

Best,
Derrick

[jimj...@gmail.com]

Hello Lara:

Did you figure out a solution for this issue. I am having the same problem.

Thanks in advance.

Jimmy Cabra García

[jimj...@gmail.com]

Dear all,

This is the solution from CIPRES:

In the files cipres generates, the input file for garli will be named infile (no extension).

If you look at the garli.conf file generated by CIPRES you will see this line

datafname = infile

 

If your garli.conf file says datafname = infile.nex the run will fail with the error message you saw.

Because the CIPRES interface controls the names, and it will name any file you upload “infile”

 

Please check and be sure this is specified correctly, so the input fiel name and the name specified in garli.conf agree.

If this does not make sense, you can send me the _jobinfo.txt file for the run, and I will take a look.

 

Best,
Mark

Best,

Jimmy

[yehim...@gmail.com]

Hi Jimmy, I’m Lena.

I have the same error with the nexus file.

ERROR: data file not found: Concatenado_Gen.nex!

I tried the option you gave us by removing the .nex extension in the Garli configuration file but it didn't work, I have the same error again.

Do you know what can be?

Thank you

Lena

[Mark Miller]

Hi Lena,

If you are using cipres, please contact me at mmi...@sdsc.edu. If you send me the file _jobinfo.txt, I can help.

If you are running locally, it means either your file name does not agree with the garliconf file, your is not at the expected location, or there is an issue with privileges (maybe it is write protected). I can't think of any other reasons off hand.

Best,

Mark

[Mark Miller]

Hi Lena,

The infile name must agree between garli.conf and CIPRES.

If you are using CIPRES, CIPRES is expecting datafname=infile

If this fails, please contact me, and send the file _jobinfo.txt from your run.

Best,

Mark

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