I submitted the docker image to challenge 2 express lane (id: 9638032) last night but the submission did not appear to be run (status has been at "RECEIVED" for over 12 hours). There is no start time/ end time/ fail reason message. I would have assumed that I would get an error message. Am I missing something? I do have a score_sc2.sh script following the example, and it is in the Dockerfile. #!/bin/sh Rscript Dry_Run_SC2.R

Created by Edward Lau edwardlau1
Dear Edward, Thanks for catching this and sorry for the inconvenience. I have fixed the bug and restarted your submission. Best, Tom
Hi Tom - thanks very much for answering my questions. My submission (syn10917780) ran finally, and it appears my prediction file was okay but the confidence file was not. The first message I got was: Your submission "syn10917780" (ID: 9638212) to the Proteogenomics Subchallenge 2 Express Lane has been scored: Your prediction file has been stored, but you will not have access to it. and the second message was: Sorry, but we were unable to validate your submission to the Proteogenomics Subchallenge 2 Express Lane. Please refer to the challenge instructions which can be found at https://www.synapse.org/#!Synapse:syn8228304/wiki/448381 and to the error message below: submission name: syn10917780 submission ID: 9638212 confidence file must be named confidence.tsv, and your model must generate confidence.tsv I checked my R script a couple of times and it did save to output/confidence.tsv. I wonder if the error could be due to some boundaries (only positive numbers allowed etc.) for confidences, since for testing purpose I simply exported my predictions twice in two different file names. Thanks for your help, Edward
Dear Edward, Great question! Simply run `chmod 770 score_sc1.sh` before you do your docker build command. It will get copied onto the image with the right permissions. Best, Tom
Ah my apologies for the premature question then. I had assumed that scoring script was automatic! Update: as I was typing this I received the below error log. I assume I have to chmod my script: 500 Server Error: Internal Server Error ("oci runtime error: container_linux.go:247: starting container process caused "exec: \"/score_sc2.sh\": permission denied" ") And wonder if anyone could provide guidance on how to do so in the Docker image. (e.g., add RUN chmod 770 score_sc1.sh to Dockerfile after the COPY lines?) Thanks! Edward
Dear Edward, Your submission should be running / ran now. Sorry about the delay. Best, Tom

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