After following all the procedure for submission of docker image itemized on https://github.com/Sage-Bionetworks-Challenges/Anti-PD1-DREAM-Examples I was able to run my docker image successful on my computer (Linux, Ubuntu 18.10 with docker 19.03.6) and was also able to save the output from synthetic data on my local. But when I submitted to the challenge I got error log ("Error collecting output for parameter 'predictions':\nAnti-PD1-DREAM-Infrastructure-master/run_docker.cwl:67:7: Did not find output file with glob pattern: '['predictions.csv']'", {}). Instead for the output/predcitions.csv to be saved to the challange resources for evaluation, the predcition output was returned to my synapse files as log.txt My docker file is attached below: FROM python:3.7 WORKDIR /project COPY dream_subchallenge2.py /project ## script that connected the three files needed for prediction and produce output COPY subchallenge2_model1.sav /project ## predictive model developed, it must be given with -m follow by file path as shown below COPY requirements.txt /project RUN pip install -r /project/requirements.txt CMD ["python", "/project/dream_subchallenge2.py", "-g", "/data", "-m", "/project/subchallenge2_model1.sav"] The commands pass with docker images are: docker run -v $(pwd)/CM_026_formatted_synthetic_data_subset/:/data:ro -v $(pwd)/output:/output:rw model:v1 Kindly help.

Created by Adeolu OGUNLEYE adeoluokiki
Thanks @vchung. Issues resolved. Initially, I created output directory within my script relative to the working directory but it didn?t work. I resolved the issue by supplying the output directory as an argument from which the directory '/output" was created. Previous commands: CMD ["python", "/project/dream_subchallenge3.py", "-g", "/data", "-m", "/project/subchallenge3_model1.sav"] New commands (this worked for me) CMD ["python", "/project/dream_subchallenge3.py", "-g", "/data", "-m", "/project/subchallenge3_model1.sav", "-o", "/output"] #output directory added to the arguments
Im having the same issue! please help
Hello, we are having the same issue/error in the OS subchallenge. In our case, we have verified the correct spelling and predictions.csv is written to /output when we run locally. We previously had no issues submitting our first try for the OS subchallenge.
Hi @adeoluokiki , That error indicates that the predictions.csv file is not found in the directory, `/output`. Are you printing your results to a file? From your comment here: > "Instead for the output/predcitions.csv to be saved to the challange resources for evaluation, the predcition output was returned to my synapse files as log.txt" it sounds like you may be printing your result to STDOUT instead? If you are printing your results to a file, then the error could be stemming from a possible typo? e.g. prediction.csv instead of predictions.csv. Finally, your question about the markdown has been answered [here](https://www.synapse.org/#!Synapse:syn18404605/discussion/threadId=7786&replyId=24186). Let me know if you have any other questions!
I discovered that some signs got missing from my docker run codes above after posting, all the $ signs in the codes disappeared and some characters were automatically converted to subscript after posting but when I clicked edit all the signs were intact and characters were normal. Why is this happening? kindly help

Exception: No 'predictions.csv' file written to /output page is loading…