EMR seems to fail always at the last step

[vlad-belogrudov]

I am getting results similar to http://www.biostars.org/p/83060/

[gecgooden]

I also get this problem, and I have noticed that the last step requires s3://crossbow-emr/dummy-input as an input but this file doesn't seem to exist. Could that be causing the error?

[val-antonescu]

Hi George,

I see the dummy-input file there. It had public access but just in case I made it public again. Can you please check once more and let me know if you can see it?

thanks in advance, Val

On 12/12/2013 10:15 PM, George Gooden wrote:

I also get this problem, and I have noticed that the last step requires s3://crossbow-emr/dummy-input as an input but this file doesn't seem to exist. Could that be causing the error?

— Reply to this email directly or view it on GitHub https://github.com/BenLangmead/crossbow/issues/6#issuecomment-30483275.

[gecgooden]

Using s3cmd, the dummy-input looks like it is just an empty folder.

 $ s3cmd ls s3://crossbow-emr/dummy-input/
    2013-07-31 19:15         0   s3://crossbow-emr/dummy-input/

George

[gecgooden]

I was able to resolve this issue by doing the following:

1. Creating a new file called dummy-input touch dummy-input
2. Uploading this file to my own bucket s3cmd put dummy-input s3://crossbow-lei/ (Available here: https://s3-us-west-2.amazonaws.com/crossbow-lei/dummy-input)
3. Running my command with cb_emr, but adding --dryrun to the end to create the json and sh files.
4. Modified the generated json file so my dummy input file was the input for the final step.
5. Ran the sh file that was generated.