Setup/Mapping not working properly

[ambarrio]

Dear Adam and others that may have found a similar problem,

After preparing my Protocol.xml, I run setup and this messages come out:

Jelly.py setup Protocol.xml
2014-08-27 11:04:03,669 [INFO] Running /home/user/glob/local/PBSuite/bin/Jelly.py setup Protocol.xml
[WARNING] Couldn't find /path/to/genome.qual... assuming there isn't a quality file for the reference
2014-08-27 11:04:03,798 [INFO] Executing Stage: setup
2014-08-27 11:04:03,915 [INFO] Finished Submitting Stage: setup

But the .sa file wasn't created (if it has to be created at this stage) and following another post of another user, I realized it is because the sawriter program from blasr was not in my path - Adam, could you include in the documentation that this program is needed?

After I repeated the setup -> mapping steps and nothing happened. I run manually the commands of the .sh files for one of my chunks and it produced the desired .m4 file. But when I get to the next stage (support) it seems that some kind of .gapInfo.bed file is not in place. How can I create that file and which program is used?

Which step is not working that is in charge of creating .sa and .gapInfo.bed? How can I fix this?

Then, I can proceed to fix the mapping because after the manual running, I tried to re-run the step and I just get this:

Jelly.py mapping Protocol.xml
2014-08-27 11:08:26,506 [INFO] Running /home/user/glob/local/PBSuite/bin/Jelly.py mapping Protocol.xml
[WARNING] Couldn't find /path/to/genome.qual... assuming there isn't a quality file for the reference
2014-08-27 11:08:26,530 [INFO] Executing Stage: mapping
2014-08-27 11:08:26,575 [INFO] Running blasr
2014-08-27 11:08:26,604 [WARNING] Output File /path/to/corrected.pb_051.chunk1.fasta.m4 already exists and will be overwritten.
2014-08-27 11:08:28,820 [INFO] Finished Submitting Stage: mapping

Thanks a lot for any input you can give me in the problem.

Best,
álvaro

[Adam English]

Hello,

Please check the detailed logs inside setup/.err or mapping/.err. You'll find more details about what went wrong.

--
~/Adam English

[ambarrio]

There is no setup/ folder created when I run "setup Protocol.xml". I am trying to pprint the variable myCommands that it is passed to self.runCmd but I get just a reference:

[INFO] Executing command: <pbsuite.utils.CommandRunner.Command instance="" at="" 0x13e1c20="">

so I don't know what's going on under the hood.

Any ideas? Thanks!

[ambarrio]

OK, I know what was my problem now. Your genome has to explicitly finish in .fasta and mine was .fa

But the setup err and out files are generated in the folder where the genome lies and not a setup one.

Cheers and thanks for the tool,
álvaro